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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Investigating Thaw and Plant Productivity Constraints on Old Soil Carbon Respiration From Permafrost

Isotopic radiocarbon (Δ 14 C) signatures of ecosystem respiration (Reco) can identify old soil carbon (C) loss and serve as an early indicator of permafrost destabilization in a warming climate. Warming also stimulates plant productivity causing plant respiration to dominate Reco Δ 14 C signatures and potentially obscuring old soil C loss. Here, we investigate how a wide spatio-temporal gradient of permafrost thaw and plant productivity affects Reco Δ 14 C patterns and isotopic partitioning. Spatial gradients came from a warming experiment with doubling thaw depth and variable biomass, and a vegetation removal manipulation to eliminate plant contributions. We sampled in August and September to capture transitions from high to low plant productivity, decreased surface soil temperature, and relatively small seasonal thaw extensions. We found that surface processes dominate spatial variation in old soil C loss and a process-based partitioning approach was crucial for constraining old soil C loss. Resampling the same plots in different times of the year revealed that old soil C losses tripled with cooling surface temperature, and the largest old soil C losses were detected when the organic-to-mineral soil horizons thawed (~50–60 cm). We suggest that the measured increase in old soil respiration over the season and when the organic-to-mineral horizon thawed, may be explained by mobilization of nitrogen that stimulates microbial decomposition at depth. Our results suggest that soil C in the organic to mineral horizon may be an important source of soil C loss as the entire Arctic region warms and could lead to nonlinearities in projected permafrost climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Fabrication of anti-adhesion surfaces on aluminium substrates of rubber plastic moulds using electrolysis plasma treatment

An anti-adhesion surface with a water contact angle of 167° was fabricated on aluminium samples of rubber plastic moulds by electrolysis plasma treatment using mixed electrolytes of C{sub 6}H{sub 5}O{sub 7}(NH{sub 4}){sub 3} and Na{sub 2}SO{sub 4}, followed by fluorination. To optimise the fabrication conditions, several important processing parameters such as the discharge voltage, discharge time, concentrations of supporting electrolyte and stearic acid ethanol solution were examined systematically. Using scanning electron microscopy (SEM) to analyse surfaces morphology, micrometer scale pits, and protrusions were found on the surface, with numerous nanometer mastoids contained in the protrusions. These binary micro/nano-scale structures, which are similar to the micro-structures of soil-burrowing animals, play a critical role in achieving low adhesion properties. Otherwise, the anti-adhesion behaviours of the resulting samples were analysed by the atomic force microscope (AFM), Fourier-transform infrared spectrophotometer (FTIR), electrons probe micro-analyzer (EPMA), optical contact angle meter, digital Vickers microhardness (Hv) tester, and electronic universal testing. The results show that the electrolysis plasma treatment does not require complex processing parameters, using a simple device, and is an environment-friendly and effective method. Under the optimised conditions, the contact angle (CA) for the modified anti-adhesion surface is up to 167°, the sliding angle (SA) is less than 2°, roughness of the sample surface is only 0.409μm. Moreover, the adhesion force and H{sub v} are 0. 9KN and 385, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry

Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the application of ultrahigh resolution mass spectrometry to profile the molecular composition of SOM and its degradation during a simulated warming experiment. A soil sample, collected near Barrow, Alaska, USA, was subjected to a 40-day incubation under anoxic conditions and analyzed before and after the incubation to determine changes of SOM composition. A CHO index based on molecular C, H, and O data was utilized to codify SOM components according to their observed degradation potentials. Compounds with a CHO index score between –1 and 0 in a water-soluble fraction (WSF) demonstrated high degradation potential, with a highest shift of CHO index occurred in the N-containing group of compounds, while similar stoichiometries in a base-soluble fraction (BSF) did not. Additionally, compared with the classical H:C vs O:C van Krevelen diagram, CHO index allowed for direct visualization of the distribution of heteroatoms such as N in the identified SOM compounds. We demonstrate that CHO index is useful not only in characterizing arctic SOM at the molecular level but also enabling quantitative description of SOM degradation, thereby facilitating incorporation of the high resolution MS datasets to future mechanistic models of SOM degradation and prediction of greenhouse gas emissions.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2021

Low soil phosphorus availability triggers maize growth stage specific rhizosphere processes leading to mineralization of organic P

Phosphorus (P) is one of the essential nutrients for all living organisms. High-quality mineral P fertilizer is a finite resource with only an estimated 80-100 years of reserves remaining globally. Both plants and microbes have developed several mechanisms such as secretion of organic acids, acidification of the rhizosphere, and production of extracellular enzymes to enhance the acquisition of P from soils. Increased activity of phosphatase occurs in response to P deficiency as part of P starvation responses which catalyze the hydrolysis of P o from soil organic matter (SOM) and release inorganic P (P i ). However, the specific interactions between plants and microbial communities in the rhizosphere soil triggered by P deficiency are largely unknown. In a greenhouse study we grew maize plants in low and high P containing soils and examined the role of rhizosphere processes on mineralization of organic P (P o ) in soils with low and high P availability and different P speciation 23 (Po dominated versus P i dominated) and determine its effect on plant growth. Plant biomass was determined and rhizosphere soils, and soil samples from pots with and without plants were collected at key vegetative growth stages (VGS). A variety of biogeochemical parameters (e.g. microbial biomass C and P, potential phosphatase activities, plant biomass P, soil P species etc.) were determined using both conventional (sequential chemical extraction) and advanced (e.g. high resolution mass spectrometry (FTICR-MS) and 3129 P solution NMR) techniques. Here, we used phospholipid fatty acid (PLFA) and DNA based microbial community analysis to track changes in microbial community structure and diversity. Low P availability induced changes in biogeochemical processes and microbial community composition in the rhizosphere soils of plants grown in low P containing soil. At early VGS, the plants in low P soil were visually struggling which correlated with greater rhizosphere potential acid phosphatase activity and a reduction in P o fractions. At late VGS, the plants appeared to recover which correlated with a decrease in Meh (III) extractable P, an increase in microbial biomass C and P and greater total P in the plant biomass (roots, shoots and leaves). In high P containing soil, on the other hand, greater P availability masked these rhizosphere processes. Our results confirmed the degradation of SOM and Po mineralization in rhizosphere soils driven by microbe and plant need for P. P deficiency may have favored the abundance of fungi which utilized easily degradable root exudates for the production of extracellular enzymes responsible for the mineralize of SOM P o . This study highlights the intertwined mechanisms involved, and emphasizes the importance of, P o sources for plant nutrition and survival in marginal soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Determining Coal Ash Impacts on Radium and Thorium Background Levels in Soil Using Rare Earth Element Analyses - 18604

One challenge at large remediation sites contaminated with radiological materials is differentiating between low-level site-related contamination and NORM. This is because sites contaminated with radiological materials, such as thorium processing and mining and milling facilities, often generate wastes that contain contaminants that are similar to NORM deposits. For sites in urban areas, this issue is further compounded due to the presence of historic industrial fill (historic fill) containing materials such as fly ash, coal ash, and red brick, that exhibit elevated radioactivity levels. These materials often have activity levels near, or even well above, a site's cleanup goal. At a large Superfund Site in the eastern US (Site), many of the suspected Site-related fill areas are commingled with coal and fly ash. As the cleanup criteria for the radionuclides of concern (ROC), radium (Ra) and thorium (Th), is 5 pico-Curies per gram above background, a four-pronged approach was developed to determine if the coal and fly ash are impacting the background levels of the ROCs. This evaluation included a review of boring logs to visually confirm the presence of historic fill, as well as coal fragments and coal ash; a literature review to establish the typical concentrations of Ra and Th found in coal and fly ash from US sources; the use of rare earth analyses to establish chemical signatures for non-Site related historic fill containing coal ash versus Site-related fill; and a quantitative analysis of Site-related data to determine if the radioactivity levels in historic fill containing coal were elevated. Soil samples were collected from two locations at the Site; fill areas containing coal ash that were not suspected to be impacted by Site activities, as well as fill areas containing coal ash that were associated with the former processing facility. These samples were analyzed for rare earth elements (REE), as well as Ra-228 and Th-232 and the ratios of lanthanum, cerium, and neodymium to Ra-228 and Th-232 were established for each sample. Based on a comparison of these data, a strong correlation was established between the rare earth/thorium decay chain ratios and the classification of material as either Site or non-Site related. These data were used to develop a higher background activity for fill areas containing non-Site related NORM. While the cleanup level defined in the Record of Decision remained unchanged, the higher background derived from the fly ash/coal ash material, as identified by REE analyses, resulted in higher project screening levels, which ensured that excavation activities did not 'chase' material that was not Site-related. To date, use of the coal ash background level has saved millions of dollars in cleanup costs since non-Site related contamination is not being remediated. Use of this approach to determine the appropriate background level for a site is relatively straightforward since it relies on visual observation of the soil for coal and fly ash, along with REE analyses, which is an inexpensive, quick, and established analytical method for soil samples. As long as a good rare earth profile of both contaminated and natural (in this case fly ash and coal ash) material can be established, the results can be quite definitive, which could result in significant volume reduction by minimizing the amount of material excavated and disposed of. This will lead to cost and time savings for what could be an otherwise costly and potentially complex excavation. Anyone performing environmental remediation of NORM contaminated sites may benefit from this paper and presentation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

An automated framework for NMR chemical shift calculations of small organic molecules

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties - specifically NMR chemical shifts in this manuscript - via the open source, high-performance omputational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model (COSMO). The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacent to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. In conclusion, these results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Reducing Contingency through Sampling at the Luckey FUSRAP Site - 13186

Typically, the greatest risk in developing accurate cost estimates for the remediation of hazardous, toxic, and radioactive waste sites is the uncertainty in the estimated volume of contaminated media requiring remediation. Efforts to address this risk in the remediation cost estimate can result in large cost contingencies that are often considered unacceptable when budgeting for site cleanups. Such was the case for the Luckey Formerly Utilized Sites Remedial Action Program (FUSRAP) site near Luckey, Ohio, which had significant uncertainty surrounding the estimated volume of site soils contaminated with radium, uranium, thorium, beryllium, and lead. Funding provided by the American Recovery and Reinvestment Act (ARRA) allowed the U.S. Army Corps of Engineers (USACE) to conduct additional environmental sampling and analysis at the Luckey Site between November 2009 and April 2010, with the objective to further delineate the horizontal and vertical extent of contaminated soils in order to reduce the uncertainty in the soil volume estimate. Investigative work included radiological, geophysical, and topographic field surveys, subsurface borings, and soil sampling. Results from the investigative sampling were used in conjunction with Argonne National Laboratory's Bayesian Approaches for Adaptive Spatial Sampling (BAASS) software to update the contaminated soil volume estimate for the site. This updated volume estimate was then used to update the project cost-to-complete estimate using the USACE Cost and Schedule Risk Analysis process, which develops cost contingencies based on project risks. An investment of $1.1 M of ARRA funds for additional investigative work resulted in a reduction of 135,000 in-situ cubic meters (177,000 in-situ cubic yards) in the estimated base volume estimate. This refinement of the estimated soil volume resulted in a $64.3 M reduction in the estimated project cost-to-complete, through a reduction in the uncertainty in the contaminated soil volume estimate and the associated contingency costs. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

BSSD 2019 Performance Metric Q4

The LANL SFA in Terrestrial Microbial Carbon Cycling aims to inform climate modeling and enable carbon management in terrestrial ecosystems by discovering widespread biological processes that control carbon storage and release in temperate biome soils. To achieve these goals, computational approaches are essential to analyze increasingly complex ‘omics’ data from microbial communities in environmental samples. The SFA continues to leverage advances in ‘omics' measurement technology and computation tools to decipher microbial community function in environmental samples. The computational approach is aligned with the recent shift in the SFA’s research approach. When the SFA began 10 years ago, computational approaches principally addressed “who is there” with extremely limited insight into function. Accessible ‘omics' data for complex soil communities were primarily amplicon DNA sequences of taxonomic or functional marker genes obtained by PCR, cloning, and Sanger sequencing. Computational tools for community analysis were nascent. Over the past decade, genome resources (DOE-Integrated Microbial Genomics database) and data acquisition increased 1000-fold, common computational pipelines for many analysis tasks have arisen, and the variety of ‘omics’ measurements has expanded to routinely include shotgun metagenomics, metatranscriptomics, and versions of metabolomics. The SFA is capitalizing on these advances while also developing new computational techniques to decipher how communities with different patterns of carbon cycling function from the species to ecosystem level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Permafrost soils and carbon cycling

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous organic carbon stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global carbon cycle and the potential vulnerability of the region's soil organic carbon (SOC) stocks to changing climatic conditions. In this review, we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils, and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of organic carbon stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this organic carbon to permafrost thaw under a warming climate. Overall, frozen conditions and cryopedogenic processes, such as cryoturbation, have slowed decomposition and enhanced the sequestration of organic carbon in permafrost-affected soils over millennial timescales. Due to the low temperatures, the organic matter in permafrost soils is often less humified than in more temperate soils, making some portion of this stored organic carbon relatively vulnerable to mineralization upon thawing of permafrost.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Laser‐ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia

Summary Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen‐fixing ability). The symbiotic interaction between legumes and nitrogen‐fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser‐ablation electrospray ionization mass spectrometry ( LAESI ‐ MS ) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI ‐ MS to explore the well characterized symbiosis between soybean ( Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum . The utilization of ion mobility separation ( IMS ) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI – IMS – MS for the rapid analysis of intact root nodules, uninfected root segments, and free‐living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI – IMS – MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean‐rhizobial symbiosis.

Stopka, Sylwia A.↗
DOE OSTI2018

Efficient derivatization of methylphosphonic and aminoethylsulfonic acids related to nerve agents simultaneously in soils using trimethyloxonium tetrafluoroborate for their enhanced, qualitative detection and identification by EI-GC–MS and GC–FPD

Trimethyloxonium tetrafluoroborate (TMO·BF 4 ) has been used here in the simultaneous derivatization of phosphonic and 2-aminoethylsulfonic acids related to nerve agents in different soils for their enhanced detection and identification by electron ionization gas chromatography-mass spectrometry (EI-GC–MS). The panel of acids consisted of five Schedule 2 phosphonic acids (methyl methylphosphonic acid, ethyl methylphosphonic acid, isopropyl methylphosphonic acid, pinacolyl methylphosphonic acid and cyclohexyl methylphosphonic acid) along with two sulfonic acids, N,N-diethyl-2-aminoethylsulfonic acid and N,N-diisopropyl-2-aminoethylsulfonic acid. The acids were converted to their corresponding methyl esters at ambient temperature when present at a 10 μg g -1 concentration in three separate soils: Virginia type A soil, Ottawa sand and Nebraska EPA soil. The concentration of the acids reflects values typically encountered during proficiency tests (PTs) administered annually by the Organisation for the Prohibition of Chemical Weapons (OPCW). Derivatization times to yield detectable signals for the methyl ester products for all the acids was found to vary among all three soil samples, however, it was found that generally the most optimal time across all the matrices involved was 3 h after the addition of TMO·BF 4 . Concomitantly, the analysis of the samples was complemented using GC coupled to flame photometric detection (GC–FPD). The inclusion of GC–FPD in the analysis yielded stronger signals for all seven methylated analytes making their detection after merely 3 h possible relative to the ones initially obtained with EI-GC–MS. Regarding the three soils employed in our study, a greater methylating efficiency was found in the Virginia type A soil and Ottawa sand yielding results that were significantly larger in magnitude to those found during the same time points for the Nebraska EPA soil sample. Prolonged reaction times (up to 72 h) were explored to find the time for the highest yield of methyl ester production were found instead to be deleterious to the process showcasing the importance of the fast yielding nature of the process specifically in situations where time-sensitive analysis is crucial (e.g. OPCW-PT).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Multi‐omics of the Soil Microbiome

TheArctic is characterized by vast amounts of carbon stored in permafrost and isan important focal point for the study of climate change as increasing temperature may accelerate microbially‐mediated release of carbon stored inpermafrost into the atmosphere as CO 2 and CH 4 . Yet surprisingly, very little is known about the vulnerability of permafrost andresponse of microorganisms in the permafrost to their changing environment. To address these knowledge gaps we used omics technologiesto explore permafrost microbial communities, to reveal hitherto unknown soilmicrobial populations and to link them to specific soil biogeochemical processes. For these projects we employed an omics pipeline that includes metagenomics, metatranscriptomics and metaproteomics to determine the phylogenetic and functional gene compositions and their expression in complex, non‐sterile soil samples collected from the field at several locations in Alaska. These studies have presented several challenges due to the unprecedented large size of the datasets and the insufficiency of available bioinformatic tools & databases to analyze, correlate and integrate thedata. To address these challenges we developed a novel functional gene databaseand used different assembly and analysis algorithms to determine key featuresin the datasets. The data reveal the microbial diversity, composition andfunctional potential in permafrost and how the microbial communities respond toclimate change impacts. Support or Funding Information Microbiomes in Transition, LDRD, Pacific Northwest National Laboratories, Richland, Washington

Jansson, Janet K.↗
DOE OSTI2024

Soil Water Percolation Chemistry, April 2017 to March 2019, BR-Ma2, Manaus

Soil water percolation chemistry including major cations, anions and isotope geochemistry. Samples were collected from six passive wick flux meters across three topographic positions (valley, slope and plateau). Data has been processed to compute the monthly mean for each topographic position where two flux meters were installed at each topographic position. All samples were processed at the Geology, Geochemistry and Geomaterials Research Laboratory (GGRL) in Los Alamos, NM USA. The metadata tab included in the .csv has additional information on locations where the sensors were installed, and other installation/maintenance details. Contact ksolander@lanl.gov if you need to use this dataset for additional information.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content

Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples. We then used high-throughput amplicon sequencing of the ITS and 16S rDNA regions to characterize these microbiomes. Leaf microbiomes were the least diverse and the most even in terms of OTU richness and abundance compared to near soil and far soil, especially in their bacterial component. Microbial composition was significantly and primarily affected by niche (leaves vs. soil) but also by soil management type and plant species in the fungal microbiome, while moisture content and pore sizes were more important drivers for the bacterial communities. The pore size effect was significantly dependent on moisture content, but only in the organic management type. Overall, our results refine our understanding of the decomposition of carbon residues in the soil and the factors that influence it, which are key for environmental sustainability and for evaluating changes in ecosystem functions.

16S rDNA↗
DOE OSTI2016

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

A deficit of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Findings showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R 2 >0.90 in all cases). Our results provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.

59 BASIC BIOLOGICAL SCIENCES↗