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Citric acid-assisted accumulation of Ni and other metals by Odontarrhena muralis: Implications for phytoextraction and metal foliar distribution assessed by μ-SXRF
Odontarrhena muralis is one of the most promissing plant species for Ni phytomining, and soil amendments can further increase its Ni phytoextraction ability. Here we investigated whether Ni phytomining/phytoremediation using this Ni hyperaccumulator can benefit from applying citric acid to a serpentine soil that is naturally enriched in Ni (>1000 mg kg -1 ). Synchrotron micro X-ray fluorescence (μ-SXRF) was used to image Ni and other metal distributions in whole fresh leaves of O. muralis. Leaf Ni accumulation in plants grown on citric acid-amended soil increased up to 55% while Co, Cr, Fe, Mn, and Zn concentrations were 4-, 14-, 6-, 7- and 1.3-fold higher than the control treatment. O. muralis presented high bioconcentration factors (leaf to soil concentration ratio) to Ni and Zn whereas Cr was seemingly excluded from uptake. The μ-SXRF images showed a uniform distribution of Ni, preferential localization of Co in the leaf tip, and clear concentration of Mn in the base of trichomes. The citric acid treatments strongly increased the Co fluoerescence intensity in the leaf tip and altered the spatial distribution of Mn across the leaf, but there was no difference in Ni fluorescence counts between the trichome-base region and the bulk leaf. Our data from a serpentine soil suggests that citrate treatment enhances Ni uptake, but Co is excreted from leaves even in low leaf concentrations, which can make Co phytoming using O. muralis unfeasible in natural serpentine soils.
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12
Abstract Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
Dynamic Responses of Trace Metal Bioaccessibility to Fluctuating Redox Conditions in Wetland Soils and Stream Sediments
Natural aquatic systems undergo fluctuating redox conditions due to microbial activity, varying water saturation levels, and nutrients dynamics. With fluctuating redox conditions, trace metals can mobilize or sequester in response to changes in iron and sulfur speciation and the concentrations and lability of organic carbon. This study examined the effect of redox fluctuations on trace metal mobility in samples collected from two different natural aquatic systems: riparian wetlands and a stream. The wetland soils contained low sulfur and total Fe contents as compared to stream sediments. The mineral composition at both sites was dominated by quartz. We incubated water-saturated soils under three cycles of anoxic-oxic conditions (τanoxic:τoxic = 3) spanning 24 days and monitored the change in dissolved and bioavailable metal concentrations. For both natural systems, reduction of iron oxides under anoxic conditions caused Co and Zn release. In contrast, oxidation of sulfides mobilized Cu under oxic conditions in both sites. In wetland soils, dissolution of Fe (hydr)oxides increased Ni solubility; however, in stream sediments, Ni release occurred when sulfides or organic matter were oxidized. For stream sediments, each subsequent redox cycle increased the bioavailability of trace metals. Redox fluctuations in wetland soils increased bioavailable Zn and Cu and decreased bioavailable Ni and Co. This study illustrates that different trace metals display distinct bioavailability patterns during redox fluctuations in natural environments. The biogeochemical cycling of nutrients in systems with redox fluctuations may be influenced by these trace metal availability patterns in addition to the availability of electron donors and acceptors.
A paradigm shift for evaluating natural attenuation of radioactive iodine in soils and sediments: Species-specific mechanisms and pathways
Not Available
Soil microbiome engineering for sustainability in a changing environment
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
Geophysical signatures of soil AFFF contamination from spectral induced polarization and low field nuclear magnetic resonance methods
Few field methods are available for characterizing source zones contaminated with aqueous film forming foam (AFFF). Non-invasive geophysical characterization of AFFF source zone contamination in situ could assist with the delineation and characterization of these sites, allowing for more informed sampling regimes aimed at quantifying subsurface poly- and perfluoroalkyl substances (PFAS) contamination. In this study, we present initial results from the investigation of the sensitivity of two existing surface and borehole-deployable geophysical technologies, spectral induced polarization (SIP), and low field nuclear magnetic resonance (NMR), to soils impacted with AFFF. To investigate the sensitivity of these methods to AFFF-impacted soil, bench-scale column experiments were conducted on samples consisting of natural and synthetic soils and groundwater. While our findings do not show strong evidence of NMR sensitivity to soil PFAS contamination, we do find evidence that SIP has sufficient sensitivity to detect PFAS sorption to soils. This finding is based on evidence that AFFF constituents associated with the pore surface produce a measurable polarization response in both freshly contaminated synthetic soils and in soils historically impacted with AFFF.
Model Soil Consortium 2 (MSC-2) Bacterial Isolate Genomes
Model Soil Consortium 2 (MSC-2) bacterial isolate genome collections are derived from the soil consortium MSC-1 multi-species cultured isolate genome collections from a previously reported WA-IsoC_MSC1.1.0 collection of a naturally evolved, model soil consortia (10.25584/WAIsoCMSC1/1635272). This collection contains 8 different isolate species cultivated under variable carbon and nitrogen sources, originating from the IAREC grassland soil field site located in Prosser, WA, USA. Genomic sequencing of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names of a given organism within a natural environment. The version described here is the first version.
Soil Microbiomes Under Climate Change and Implications for Carbon Cycling
Communities of soil microorganisms (soil microbiomes) play a major role in biogeochemical cycles and support of plant growth. Here we focus primarily on the roles that the soil microbiome plays in cycling soil organic carbon and the impact of climate change on the soil carbon cycle. We first discuss current challenges in understanding the roles carried out by highly diverse and heterogeneous soil microbiomes and review existing knowledge gaps in understanding how climate change will impact soil carbon cycling by the soil microbiome. Because soil microbiome stability is a key metric to understand as the climate changes, we discuss different aspects of stability, including resistance, resilience, and functional redundancy. We then review recent research pertaining to the impact of major climate perturbations on the soil microbiome and the functions that they carry out. Finally, we review new experimental methodologies and modeling approaches under development that should facilitate our understanding of the complex nature of the soil microbiome to better predict its future responses to climate change.
Fe-Coated Optical Fiber for Distributed Corrosion Monitoring in Soil and Aqueous Environment
Natural gas pipeline corrosion represents a substantial cost and safety concern during normal operations. The effective and real-time monitoring of corrosion is important to detect and mitigate pipeline risks before corrosion-related catastrophic events happen. Here, we describe the use of iron (Fe) coated optical fiber sensors (OFS) for distributed corrosion monitoring where Fe acts as a corrosion proxy. By using an optical backscattering reflectometer (OBR), corrosion was monitored based on the increase in the backscattered intensity amplitude of the light being passed as Fe underwent corrosion. The Fe-coated OFSs were prepared with a film thickness between 25–225 nanometers (nm) by an electroless plating approach and corroded by a carbon dioxide (CO2)-saturated acidic electrolyte. The corrosion rate (CR) was approximately 2.5 millimeters (mm)/year for Fe with a film thickness of 30 nm and increased with film thickness. Backscattering-based CRs were supported by visible light transmission measurements, which have been previously demonstrated. Additionally, a correlation between the intermittent transmission and residual Fe film thickness during the corrosion of Fe was established. The corrosion sensor was also tested in soil at > 1 foot depth. Fe-coated OFS was loaded into a Draka cable, which provides mechanical support during fiber deployment and installation into either acidified soil, top-soil, or sandy soil (50/50).
Fe-Coated Optical Fiber for Distributed Corrosion Monitoring in Soil and Aqueous Environments
Natural gas pipeline corrosion represents a substantial cost and safety concern during normal operations. The effective and real-time monitoring of corrosion is important to detect and mitigate pipeline risks before corrosion-related catastrophic events happen. Here, we describe the use of iron (Fe) coated optical fiber sensors (OFS) for distributed corrosion monitoring where Fe acts as a corrosion proxy. By using an optical backscattering reflectometer (OBR), corrosion was monitored based on the increase in the backscattered intensity amplitude of the light being passed as Fe underwent corrosion. The Fe-coated OFSs were prepared with a film thickness between 25–225 nanometers (nm) by an electroless plating approach and corroded by a carbon dioxide (CO2)-saturated acidic electrolyte. The corrosion rate (CR) was approximately 2.5 millimeters (mm)/year for Fe with a film thickness of 30 nm and increased with film thickness. Backscattering-based CRs were supported by visible light transmission measurements, which have been previously demonstrated. Additionally, a correlation between the intermittent transmission and residual Fe film thickness during the corrosion of Fe was established. The corrosion was measurable out to > 100 meters (m), which is a significant improvement over our previous work, which showed corrosion sensing at < 10 m. The corrosion sensor was also tested in soil at > 1 foot depth.
Deeper snow increases the net soil organic carbon accrual rate in moist acidic tussock tundra: 210Pb evidence from Arctic Alaska
The net change in the carbon inventory of arctic tundra remains uncertain as global warming leads to shifts in arctic water and carbon cycles. To better understand the response of arctic tundra carbon to changes in winter precipitation amount, we investigated soil depth profiles of carbon concentration and radionuclide activities ( 7 Be, 137 Cs, 210 Pb, and 241 Am) in the active layer of a twenty-two-year winter snow depth manipulation experiment in moist acidic tussock tundra at Toolik Lake, Alaska. Depth correlations of cumulative carbon dry mass (g cm -2 ) vs. unsupported 210 Pb activity (mBq g -1 ) were examined using a modified constant rate of supply (CRS) model. Results were best fit by two-slope CRS models indicating an apparent step temporal increase in the accumulation rate of soil organic carbon. Most of the best-fit model chronologies indicated that the increase in carbon accumulation rate apparently began and persisted after snow fence construction in 1994. The inhomogeneous nature of permafrost soils and their relatively low net carbon accumulation rates make it challenging to establish robust chronologic records. Nonetheless, the data obtained in this study support a decadal-scale increase in net soil organic carbon accumulation rate in the active layer of arctic moist acidic tussock tundra under conditions of increased winter precipitation.
Fe Coated Optical Fiber for Distributed Corrosion Monitoring in Soil and Aqueous Environment
Natural gas pipeline corrosion represents a substantial cost and safety concern during normal operations. Effective monitoring of corrosion is important to detect and mitigate pipeline risks before corrosion-related catastrophic events happen. Here, we describe the use of Fe-coated optical fiber sensors (OFS) for distributed corrosion monitoring where Fe acts as a corrosion proxy. By using an optical backscatterring reflectometer (OBR), corrosion was monitored based on the increase in backscattered intensity amplitude of the light being passed as Fe undergoes corrosion. The Fe-coated OFSs were prepared with a film thickness between 25-225 nm by an electroless plating approach and corroded by a CO2-saturated acidic electrolyte. The corrosion rate was approximately 2.5 mm/yr for Fe with a film thickness of 30 nm and increased with film thickness. Backscattering-based corrosion rates were supported by visible light transmission measurements, which have been previously demonstrated. Additionally, a correlation between the intermittent transmission and residual Fe film thickness during corrosion of Fe was established. Corrosion was measurable out to > 100 m which is a significant improvement over our previous work showing corrosion sensing at < 10 m. The corrosion sensor was also tested in soil at >1 ft depth. Fe-coated OFS was loaded into a Draka cable which provides mechanical support during fiber deployment and installation into either acidified soil, top-soil, or sandy soil.
Fe-Coated Optical Fiber for Distributed Corrosion Monitoring in Soil and Aqueous Environments
Natural gas pipeline corrosion represents a substantial cost and safety concern during normal operations. The effective and real-time monitoring of corrosion is important to detect and mitigate pipeline risks before corrosion-related catastrophic events happen. Here, we describe the use of iron (Fe) coated optical fiber sensors (OFS) for distributed corrosion monitoring where Fe acts as a corrosion proxy. By using an optical backscattering reflectometer (OBR), corrosion was monitored based on the increase in the backscattered intensity amplitude of the light being passed as Fe underwent corrosion. The Fe-coated OFSs were prepared with a film thickness between 25–225 nanometers (nm) by an electroless plating approach and corroded by a carbon dioxide (CO2)-saturated acidic electrolyte. The corrosion rate (CR) was approximately 2.5 millimeters (mm)/year for Fe with a film thickness of 30 nm and increased with film thickness. Backscattering-based CRs were supported by visible light transmission measurements, which have been previously demonstrated. Additionally, a correlation between the intermittent transmission and residual Fe film thickness during the corrosion of Fe was established. The corrosion was measurable out to > 100 meters (m), which is a significant improvement over our previous work, which showed corrosion sensing at < 10 m. The corrosion sensor was also tested in soil at > 1 foot depth.
Pangenomes suggest ecological-evolutionary responses to experimental soil warming
ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.
Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components
Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a method with which sources of environmental variation in field data can be identified and adjusted, improving our ability to resolve effects of interest and to quantify subtle phenotypes.
Quantifying the effects of switchgrass ( Panicum virgatum ) on deep organic C stocks using natural abundance 14 C in three marginal soils
Not Available
Intra-annual variation in microclimatic conditions in relation to vegetation type and structure in two tropical dry forests undergoing secondary succession
Microclimate acts as a strong filter on species performance in restored and regenerating forests, particularly in seasonally dry tropical forests (SDTF). Yet few studies have measured microclimate patterns across succession in SDTF. Furthermore, although dynamic vegetation models simulate microclimate, evaluation of these simulated variables with field observations has been relatively uncommon. Here, we investigated the seasonal patterns of soil temperature and soil water in naturally regenerated and planted successional vegetation in SDTF in Costa Rica and Puerto Rico, using complementary approaches of intensive field observations and simulation modeling with the Ecosystem Demography model. We found that plots representing later successional stages were wetter on average, but only during the dry season. During the wet season, mean soil water did not differ across vegetation types, but open, early successional vegetation experienced more frequent extreme wet and dry conditions than older forest and plantations. Soil temperature tended to decline with forest structure, and later successional vegetation also experienced less extreme daily temperature fluctuations. Basal area and leaf area index were the best predictors of differences in soil water and temperature across plots. Model simulations were consistent with observations of wet season soil temperature and soil water, but the model failed to reproduce dry season soil moisture dynamics, suggesting that further work is needed to reduce model biases in microclimate variables. Collectively, our results imply that common assumptions about how microclimates influence successional processes in SDTF should be revisited.