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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Glacier ice archives nearly 15,000-year-old microbes and phages

Background Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. Results We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants. Conclusions Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of experimental and seasonal drying on soil microbial biomass and nutrient cycling in four lowland tropical forests

Changes in precipitation represent a major effect of climate change on tropical forests, which contain some of the earth’s largest terrestrial carbon (C) stocks. Such changes are expected to influence microbes, nutrients, and the fate of C in tropical forest soils. To explore this, we assessed soil microbial biomass, potential extracellular enzyme activities, and nutrient availability in a partial throughfall exclusion experiment in four seasonal lowland tropical humid forests in Panama with wide variation in precipitation and soil fertility. We hypothesized that throughfall exclusion would reduce microbial biomass and activity and accentuate dry season soil nutrient accumulation, with larger effects in wetter, less droughtresistant forests. We observed a baseline seasonal pattern of decreased microbial biomass and increased extractable dissolved organic C (DOC), total dissolved nitrogen (TDN), nitrate (NO 3 – ), and resinextractable phosphorus (P) in the dry season, with the strongest patterns for nitrogen (N). However, potential enzyme activities showed no consistent seasonality. In line with seasonal drying, throughfall exclusion decreased soil microbial biomass in the wet season and increased TDN and NO 3 – , especially in the dry season. In contrast to seasonal drying, throughfall exclusion decreased DOC and did not affect resinextractable P, but slightly decreased potential phosphatase activities. Potential enzyme activities varied among sites and sampling times, but did not explain much variation in microbial biomass or substrate availability. We conclude that reduced rainfall in tropical forests might accentuate some dry season patterns, like reductions in microbial biomass and accumulation of extractable nutrients. However, our data also suggest new patterns, like reduced inputs of DOC to soils with drying, which could have cascading effects on soil ecological function and C storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2021

Differential Organic Carbon Mineralization Responses to Soil Moisture in Three Different Soil Orders Under Mixed Forested System

Soil microbial respiration is one of the largest sources of carbon (C) emissions to the atmosphere in terrestrial ecosystems, which is strongly dependent on multiple environmental variables including soil moisture. Soil moisture content is strongly dependent on soil texture, and the combined effects of texture and moisture on microbial respiration are complex and less explored. Therefore, this study examines the effects of soil moisture on the mineralization of soil organic C Soil organic carbon in three different soils, Ultisol, Alfisol and Vertisol, collected from mixed forests of Georgia, Missouri, and Texas, United States , respectively. A laboratory microcosm experiment was conducted for 90 days under different moisture regimes. Soil respiration was measured weekly, and destructive harvests were conducted at 1, 15, 60, and 90 days after incubation to determine extractable organic C (EOC), phospholipid fatty acid based microbial community, and C-acquiring hydrolytic extracellular enzyme activities (EEA). The highest cumulative respiration in Ultisol was observed at 50% water holding capacity (WHC), in Alfisol at 100% water holding capacity, and in Vertisol at 175% WHC. The trends in Extractable Organic Carbon were opposite to that of cumulative microbial respiration as the moisture levels showing the highest respiration showed the lowest EOC concentration in all soil types. Also, extracellular enzyme activities increased with increase in soil moisture in all soils, however, respiration and EEA showed a decoupled relationship in Ultisol and Alfisol soils. Soil moisture differences did not influence microbial community composition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Co-located temperature and electrical resistivity measurements for permafrost mapping, Teller 27, Teller 47 and Kougarok 64, Seward Peninsula, Alaska, late summers of 2018, 2019, 2021, and 2022

This data set contains co-located shallow soil (0.8m below ground level) and electrical resistivity at various depth extracted from Electrical Resistivity Tomography (ERT) measurements. Data were acquired at three watersheds on the southern Seward Peninsula during the late summers of 2018, 2019, 2021, and 2022. The three watersheds are located along the Nome-Teller Highway at mile markers 27 and 47, and along Kougarok Road mile marker 64. The co-located temperature and electrical resistivity data were used to (1) map the spatial extend of near surface permafrost, and (2) for supervised classification of permafrost bodies. This dataset contains .csv, .txt, .srv files and flmd reporting format with data dictionary. Find information about the .srv files at "https://e4d-userguide.pnnl.gov/e4d_guide/elec/e4d_e4d-survey.html". The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2016

Extraction and Capture of Water from Martian Regolith Experimental Proof-of-Concept

Mars Design Reference Architecture 5.0:Lists in-situ resource utilization (ISRU) as enabling for robust human Mars missionsLO2LCH4 ascent propulsion 25,000 kg oxygen from atmosphere for ascent and life support Atmospheric based ISRU processes less operationally complex than surface based limited concept evaluation to date and Mars surface water property and distribution uncertainty would not allow [Mars soil water processing] to be base lined at this time Limited Concept Evaluation to Date Lunar regolith O2 extraction processing experience Lunar regolith is fluidized and heated to high temperatures with H2 to produce H2O from iron-bearing minerals Mars similarity concept: Soil placed in fluidized bed reactor Heated to moderate temperatures Inert gas flow used to fluidize the bed and help with water desorption Challenges: High-temperature dusty seals Working gas requires downstream separation and recycling to reduce consumables loss Batch process heating thermally inefficient.

in situ resource utilization↗
DOE OSTI2020

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Utilization of on-site resources for Regenerative Life Support Systems at a lunar outpost

Regenerative life support systems (RLSS) will be required to regenerate air, water, and wastes, and to produce food for human consumption during long-duration stays on the moon. It may be possible to supplement some of the materials needed for RLSS from resources on the moon. Natural materials at the lunar surface may be used for a variety of lunar RLSS needs, including (i) soils or solid-support substrates for plant growth, (ii) sources for extraction of essential, plant-growth nutrients, (iii) substrates for microbial populations in the degradation of wastes, (iv) sources of O2 and H, which may be used to manufacture water, (v) feed stock materials for the synthesis of useful minerals (e.g., molecular sieves), and (vi) shielding materials surrounding the outpost structure to protect humans, plants, and microorganisms from harmful radiation.

Ming, D. W.↗
NASA NTRS1993

Utilization of on-site resources for regenerative life support systems at Lunar and Martian outposts

Lunar and martian materials can be processed and used at planetary outposts to reduce the need (and thus the cost) of transportng supplies from Earth. A variety of uses for indigenous, on-site materials have been suggested, including uses as rocket propellants, construction materials, and life support materials. Utilization of on-site resources will supplement Regenerative Life Support Systems (RLSS) that will be needed to regenerate air, water, wastes, and to produce food (e.g., plants) for human consumption during long-duration space missions. Natural materials on the Moon and/or Mars may be used for a variety of RLSS needs including (1) soils or solid-support substrate for plant growth, (2) sources for extraction of essential plant-growth nutrients, (3) sources of O2, H2, CO2, and water, (4) substrates for microbial populations in the degradation of wastes, and (5) shielding materials surrounding outpost structures to protect humans, plants, and microorganisms from radiation. In addition to the regolith, the martian atmosphere will provide additional resources at a Mars outpost, including water, CO2 and other atmospheric gases.

Ming, Douglas W.↗
NASA NTRS2008

Analysis of 6.4 KEV Moessbauer Spectra Obtained with MIMOS II on MER on Cobbles at Meridiani Planum, Mars and Considerations on Penetration Depths

The miniaturized Moessbauer (MB) spectrometers MIMOS II [1] on board of the two Mars Exploration Rovers Spirit and Opportunity have obtained more than 600 spectra of more than 300 different rock and soil targets [2-7]. Both instruments have simultaneously collected 6.4 keV X-ray and 14.4 keV .-ray spectra in backscattering geometry [1]. With Spirit's MB spectrometer, 6.4 keV and 14.4 keV spectra have been obtained for all targets through sol 461. After this date, only 14.4 keV spectra were collected. With Opportunity's spectrometer, 6.4 keV and 14.4 keV spectra have been collected for all targets to date. The Fe-mineralogy of rock and soil targets at both landing sites reported to date has been exclusively extracted from 14.4 keV spectra [2-5]. The comparison of 6.4 keV and 14.4 keV spectra provides depth selective information about a sample, but interpretation is not always straightforward [8].

Fleischer, I.↗
NASA NTRS2018

ISRU Technology Development for Extraction of Water from the Mars Surface

Goals: Develop technologies to extract water from planetary regolith considering production rate vs: energy/power consumption (efficiency, yield, heat recuperation options); Mass and sizing: modularity, batch sizes, soil feed options, etc.; Ruggedness in terms of soil, environmental, and operational parameters; seals and component wear, etc.; Removal of product and disposal of spent material. Summary: Technology development is underway for several ISRU water extraction hardware concepts for Mars application - Hydrated minerals (Auger dryer, Microwave, Open Air), Subsurface Ice (Rodwell); Models are developed with experimental and breadboard efforts for use in larger ISRU system models; Each effort consists of a 3 year development plan, with the goal of integrating into a larger subsystem test in 2020 - Concurrent technology advance allows for flexibility in system design; depending on architecture decisions and progress of associated subsystems.

In-Situ Resource Utilization↗
NASA NTRSDate not supplied

Quantifying Leak Rates and Vacuum Impact on Granular Soil Column Pneumatic Seal

Introduction: All In-Situ Resource Utilization (ISRU) regolith reactor systems that aim to extract gases or vapors must maintain a seal along the flow path of the regolith from the inlet hopper to where extracted gases or vapors are generated. Using a column of regolith at the inlet has been proposed as an alternative to systems using series of mechanical valves to reduce mass and complexity. Preliminary investigations into the use of regolith itself as a barrier to escaping fluids have been conducted, which this research seeks to expand upon. Different vertical regolith simulant plug diameters and heights were tested under vacuum with dry nitrogen to observe leak rates and approximate steady state pressure gradient equilibria. The effect of absolute ambient pressure was also studied by repeating tests at incremental pressures ranging from 10e-5 Torr up to 1 atm to corroborate ambient bench tests from previous work. The impact of regolith dynamics was addressed to emulate continuous-feed regolith reaction processes by measuring leak rates through continuously draining simulant columns. OB-1 lunar highlands regolith simulant was used. Experimental Setup: Regolith simulant columns were constructed using a motorized butterfly valve separating upper acrylic tubes of various diameters from a larger, lower aluminum pipe plenum (See Figure 1). The butterfly valve was cracked open such that gas could freely pass through whereas regolith would bridge and stay suspended as a cohesive plug above in the acrylic portion. These assemblies were loaded into a vacuum chamber, and a compressed dry nitrogen line was routed into the lower plenum. Pressure transducers measured the absolute pressure of the lower plenum, which was compared to absolute chamber pressure to monitor the pressure gradient across the regolith simulant. A precision mass flow controller enabled fine control of plenum pressure. The plenum pressure was quasi-statically increased to set points informed by previous work [1] before shutting off the gas supply to allow the now pressurized gas volume to dissipate through the simulant into the chamber in what was referred to as a ‘leak test.’ In a separate set of tests, the pressure was allowed to quasi-statically build until visual disturbances in the soil were observed via remote camera feeds. Initial leak rate tests were repeated on the disturbed soil to observe changes in leak rates between initial as-poured and post-bubbling soil conditions. This test schedule was applied to simulant columns of three different diameters (approximately 2, 4, and 6 inches) as well as two different heights (around 8 and 16 inches) and was repeated at least three times for each configuration. Plenums were also pressurized while the butterfly valves were opened slightly further to facilitate slow, controlled, constant flowrate draining of the simulant to observe the impact that continuous-feed systems might have on leak rate through the regolith column. Finally, the regolith columns were reset and refilled and static leak rate tests were repeated approximately every decade in ambient pressure from 10e-5 Torr up to ambient conditions to observe the impact of transitioning out of the molecular flow regime on regolith column seal performance. Analysis: Trends with respect to each factor examined were constructed and reported alongside commentary on the most likely responsible physical phenomena. Confidence intervals were applied to the predictive findings of the data by quantifying instrumentation error and accounting for probabilistic impacts of curve fitting the generic exponential function onto pressure decay data. The leak rate is assumed directly proportional to the exponential term coefficient, while the steady-state static pressure gradient is assumed to be the asymptotic limit of each curve fit. Finally, a generic model developed by Ogino et al. [2] and later tuned for ambient testing was re-tuned using vacuum data to estimate leak rates on the lunar surface. Results: Pressure decay rates decreased up to 27-fold under vacuum when compared to ambient pressure, as shown in Figure 2. Simulant column diameter was found to exponentially correlate to both regolith column leak rate and steady-state equilibrium pressure delta. Height was found to be linearly related to leak rate –doubling the regolith column height consistently yielded around a 40% reduction in leak rate. Dynamic regolith draining was found to slightly increase leak rate, although to a lower degree than expected. Conclusion: Because of the transition into molecular gas flow through regolith, vacuum testing is required to properly estimate performance. Regolith columns should be designed as narrow as possible to avoid bridging and minimize leak rate, and as tall as is feasible to both further reduce leak rate and to help prevent bubbling, which has been shown to degrade the quality of the regolith seal. Disrupted soil was found to exhibit higher leak rates than pristine, as-poured soil, indicating the need to consider the impact of recovery from depressurization events. Regolith columns appear equally feasible for both dosed and continuous-feed reactors.

ISRU↗
NASA NTRS2016

Assimilation of SMOS Brightness Temperatures or Soil Moisture Retrievals into a Land Surface Model

Three different data products from the Soil Moisture Ocean Salinity (SMOS) mission are assimilated separately into the Goddard Earth Observing System Model, version 5 (GEOS-5) to improve estimates of surface and root-zone soil moisture. The first product consists of multi-angle, dual-polarization brightness temperature (Tb) observations at the bottom of the atmosphere extracted from Level 1 data. The second product is a derived SMOS Tb product that mimics the data at a 40 degree incidence angle from the Soil Moisture Active Passive (SMAP) mission. The third product is the operational SMOS Level 2 surface soil moisture (SM) retrieval product. The assimilation system uses a spatially distributed ensemble Kalman filter (EnKF) with seasonally varying climatological bias mitigation for Tb assimilation, whereas a time-invariant cumulative density function matching is used for SM retrieval assimilation. All assimilation experiments improve the soil moisture estimates compared to model-only simulations in terms of unbiased root-mean-square differences and anomaly correlations during the period from 1 July 2010 to 1 May 2015 and for 187 sites across the US. Especially in areas where the satellite data are most sensitive to surface soil moisture, large skill improvements (e.g., an increase in the anomaly correlation by 0.1) are found in the surface soil moisture. The domain-average surface and root-zone skill metrics are similar among the various assimilation experiments, but large differences in skill are found locally. The observation-minus-forecast residuals and analysis increments reveal large differences in how the observations add value in the Tb and SM retrieval assimilation systems. The distinct patterns of these diagnostics in the two systems reflect observation and model errors patterns that are not well captured in the assigned EnKF error parameters. Consequently, a localized optimization of the EnKF error parameters is needed to further improve Tb or SM retrieval assimilation.

SMOS↗
DOE OSTI2021

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Lignin is nature’s largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter , Aminobacter , Bacillus , Burkholderia , Lysinibacillus , Microvirga , Mycobacterium , Ochrobactrum , Paenibacillus , Pseudomonas , Pseudoxanthomonas , Rhizobiales and Sphingobium . These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data for "Soil carbon dynamics during drying vs. rewetting: Importance of antecedent moisture conditions"

This dataset contains data used for the paper "Soil carbon dynamics during drying vs. rewetting: importance of antecedent moisture conditions". The Related References field will be updated with a full citation when available.Soil moisture influences soil carbon dynamics, including microbial growth and respiration. The response of such ‘soil respiration’ to moisture changes is generally assumed to be linear and reversible, i.e. to depend only on the current moisture state. Current models thus do not account for antecedent soil moisture conditions when determining soil respiration or the available substrate pool. We conducted a laboratory incubation to determine how the antecedent conditions of drought and flood influenced soil organic matter (SOM) chemistry, bioavailability, and respiration. We sampled soils from an upland coastal forest, Beaver Creek, WA USA, and subjected them to drying and rewetting treatments. For the drying treatment, field moist soils were saturated and then dried to 75, 50, 35, and 5 % saturation. In the rewetting treatment, field moist soils were air-dried and then rewet to 35, 50, 75, and 100 % saturation. We measured respiration and water extractable organic carbon (WEOC) concentrations and used 1H-NMR and FT-ICR-MS to characterize the WEOC pool across the treatments. The drying vs. wetting treatment strongly influenced SOM bioavailability, as rewet soils (with antecedent drought) had greater WEOC concentrations and respiration fluxes compared to the drying soils (with antecedent flood). In addition, air-dry soils had the highest WEOC concentrations, and the NMR-resolved peaks showed a strong contribution of protein groups in these soils. Both NMR and FT-ICR-MS analyses indicated increased contribution of complex aromatic groups/molecules in the rewet soils, compared to the drying soils. We suggest that drying introduced organic matter into the WEOC pool via desorption of aromatic molecules and/or by microbial cell lysis, and this stimulated microbial mineralization rates. Our work indicates that even short-term shifts in antecedent moisture conditions can strongly influence soil C dynamics at the core scale. The predictive uncertainties in current soil models may be reduced by a more accurate representation of soil water and C persistence that includes a mechanistic and quantitative understanding of the impact of antecedent moisture conditions.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv and .txt format, which can be accessed and processed using MS Excel or R. NMR data are provided as raw output data (accessed in Bruker TopSpin or MestreNova) as well as the MestreNova-processed files. This archive can also be accessed on GitHub at https://github.com/kaizadp/hysteresis_and_soil_carbon (DOI: 10.5281/zenodo.4432885).

1H-NMR↗
DOE OSTI2024

Differential Organic Carbon Mineralization Responses to Soil Moisture in Three Different Soil Orders Under Mixed Forested System: Supporting Data

This data contains data from 90-day long incubation study which aimed to look at the soil moisture-texture relationship on soil organic carbon (SOC) cycling. Soils were collected from three distinct soil textures from mixed forests in 2017: sandy (Georgia, 2017-05-01), loamy (Missouri, 2017-06-14) and clayey (Texas, December 2017) were incubated at different soil moisture levels (air-dried, 25% water holding capacity (WHC), 50% WHC, 100% WHC and 175% WHC) at room temperature for a period of 90 days. Files contain microbial respiration, active and slow SOC pools, and their respective mineralization rates, extractable organic carbon (C), and C-acquiring extracellular enzymes. Findings from these data were used in Singh et al. (2021). This study aimed to examine the interactive effect of soil moisture and texture on SOC mineralization. Soil samples of three distinct textures (sandy, loamy, and clayey) were collected from mixed forests of Georgia, Missouri, and Texas, respectively. Soil cores of 5 cm diameter were collected from numerous random locations at each site from 0-15 cm depth after scraping the litter layer and mixed thoroughly to obtain a composite sample per site. Three additional soil cores were collected to determine the WHC using pressure plate extractors. Soil samples were composited, and triplicate soil samples were incubated in mason jars for a period of 90 days at room temperature under different moisture regimes: air dried, 25% WHC, 50% WHC, at WHC and 100% saturation. Soil respiration was measured weekly, and destructive sampling was conducted at 1, 15, 60, and 90 days to determine extractable organic C, C acquiring enzyme activity, and active and slow SOC pools with their respective mineralization rates. The C acquiring enzyme activity was the total activity of α-glucosidase, β-glucosidase, cellobiohydrolase, and β-xylosidase enzymes. Gas samples for microbial respiration measurements were collected from headspace of incubation jars through the sampling ports on the lids and then analyzed using a Shimadzu Gas Chromatograph (GC-2014). Prior to sampling, the vials were evacuated. Blank correction was also done by collecting gas samples from empty incubation jars. Double pool exponential decay model was used in SigmaPlot to determine the active and slow SOC pools and their mineralization rates (Farrar et al., 2012; Jagadamma et al., 2014). The C-acquiring extracellular enzymes were measured using the microplate method by German et al., (2011). Microbial community structure was determined using the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) analyses (Buyer and Sasser, 2012). This dataset has seven data files provided in comma-separate (*.csv) format. Additional metadata are provided: seven data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

Carbon acquiring enzyme activity↗