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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS2005

Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0.6-0.7 x 0.9-1.5 microm. Growth occurred within the pH range 6.5-9.5 with optimum growth at pH 7.3-7.5. The temperature range for growth of the novel isolate was 0-28 degrees C and optimum growth occurred at 24 degrees C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0.5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99.8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA-DNA hybridization between them demonstrated 39+/-1.5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

Gram-Positive Asporogenous Rods/classification/gen↗
NASA NTRS2004

Effects of drying on nitrification activity in zeoponic medium used for long-term space missions

One component of a proposed life support system is the use of zeoponic substrates, which slowly release NH4+ into "soil" solution, for the production of plants. Nitrifying bacteria that convert NH4+ to NO3- are among the important microbial components of these systems. Survival of nitrifying bacteria in dry zeoponic substrates is needed, because the substrate would likely be stored in an air-dry state between croppings. Substrate was enriched for nitrifying bacteria and allowed to air-dry in a laminar flow hood. Stored substrate was analyzed for nitrifier survivability by measuring nitrifier activity at the beginning, 3 days, 1, 2, and 3 weeks. After rewetting, activity was approximately 9 micrograms N g-1 h-1 regardless of storage time. Nitrification rates did not decrease during storage. It seems unlikely that drying between plantings would result in practical reductions in nitrification, and reinoculation with nitrifying bacteria would not be necessary.

Non-NASA Center↗
NASA NTRS2005

Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

Pinus/growth & development/physiology↗
DOE OSTI2021

Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle

Abstract With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential

Chemicals involved in plutonium uranium reduction extraction (PUREX) can be released from nuclear reprocessing facilities and accumulate in the environment. We exposed chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. The responses of soil microbial communities are dependent on soil type, and tributyl phosphate exposure generates the most reproducible changes in microbial communities. We reconstructed the genomes of key bacteria and find several phosphotriesterase genes found only in Rhizobiaceae. The abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. In conclusion, these phosphotriesterase genes may be involved in breakdown of tributyl phosphate, and a means of accessing phosphate for these bacteria.

Bioremediation↗
NASA NTRS1974

Project environmental microbiology as related to planetary quarantine

Microbiological analyses of soil particles allow for the following conclusions: (1) there is a considerable range in the values of aerobic, mesophilic microbial counts associated with different size soil fractions; (2) as soil particle size increases, there is an increase in the mean microbial concentration per particle; (3) plate counts of aerobic, mesophilic organisms in unheated soils yielded a mean concentration of about six organisms per particle for the smallest soil fraction; (4) aerobic, mesophilic counts for sonicated particles heated at 80 C for 20 minutes yielded mean values of about two organisms per particle for the smallest particles; (5) some actinomycetes associated with the soil fractions could survive dry heat treatment at 110 C for one hour; and (6) soil particles stored under ambient laboratory conditions for 2.5 years aerobic, mesophilic plate counts which were comparable or slightly greater than the counts for more recently collected soil.

Pflug, I. J.↗
NASA NTRS2003

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties. c2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

NASA Discipline Life Support Systems↗
DOE OSTI2025

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

Community Structure and Diversity↗
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

Kinetic and temperature sensitivity properties of soil exoenzymes through the soil profile down to one-meter depth at a temperate coniferous forest (Blodgett, CA)

This dataset contains data on kinetic and temperature sensitivity parameters of the exoenzymes β-glucosidase (BG), leucine/leucyl aminopeptidase (LAP) and acid phosphatase (AP) across a soil profile down to 90 cm depth at Blodgett forest, CA, USA. These data were generated to determine if kinetic and thermal properties of microbial exoenzymes involved in organic matter decomposition varied with soil depth, following variation in soil properties and microbial communities, as part of the study: Alves et al. (2021). Kinetic Properties of Microbial Exoenzymes Vary with Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Frontiers in Microbiology 12:3618. https://doi.org/10.3389/fmicb.2021.735282. This research was performed within the framework of the TES Belowground Biogeochemistry SFA project, in particular association with a long-term field warming experiment of the whole soil profile at Blodgett forest. Samples for this work were collected from locations representative of the field experimental plots. Potential enzyme activity rates were measured using laboratory fluorometric assays with soils collected at 0-10, 10-20, 30-40, 50-60, 60-70 and 80-90 cm deep in biological triplicates (i.e., three soil cores collected at different representative locations). Assays with each soil were conducted over a gradient of eight substrate concentrations per enzyme, and incubated at 4, 10, 16, 25, 35 or 50°C. Enzyme Michaelis-Menten kinetics were modeled over the eight substrate concentrations at each temperature, and the temperature sensitivity of the kinetic parameters was modeled over the six temperatures using linear Arrhenius/Q10 and non-linear Macromolecular Rate Theory (MMRT) models. The dataset includes the fully processed enzyme activity rate data used to model Michaelis-Menten kinetics, calculated kinetic and temperature sensitivity parameters, and basic soil and microbial biomass chemistry for each sample. All data is provided for each individual biological replicate, and kinetic and temperature sensitivity parameters are also provided as means of the biological replicates. The dataset also includes all raw measurement data and code used to parse, combine and perform the analyses described by Alves et al. (2021). For file descriptions, see the file-level metadata files: “enzymes_dataProcessed_flmd.xlsx” (processed data); “enzymes_dataRaw_flmd.xlsx” (compressed raw data and metadata); and “enzymes_code_flmd.xlsx” (compressed code). The experimental design, list of parameters measured, soil and microbial biomass chemistry data, and means of biological replicates for kinetic and temperature sensitivity parameters are also provided as human-readable tables in file “enzymeTraits_design_results_tables.xlsx”.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Biogeochemical Processes Across Aquatic Interfaces

The aquatic interfaces exposing terrestrial soils to oxic-anoxic regime shifts represent biogeochemical “hotspots” that are extremely sensitive to climate and environmental change. However, processes and interaction across theses aquatic interfaces are poorly understood and underrepresented in current Earth system models. In this project, we aim to develop predictive understanding of the feedbacks between microbial systems and geochemical environments that determine emergent ecosystem behaviors and resilience in response to disturbances. We use experimental, mechanistic modeling and meta-analysis tools to elucidate interactions among soil, water, geomorphology and microbiology that regulate the molecular transformations and fluxes of carbon, nutrients, and redox-sensitive compounds across aquatic interfaces.

58 GEOSCIENCES↗
NASA NTRS1989

Lunar base agriculture: Soils for plant growth

This work provides information on research and experimentation concerning various aspects of food production in space and particularly on the moon. Options for human settlement of the moon and Mars and strategies for a lunar base are discussed. The lunar environment, including the mineralogical and chemical properties of lunar regolith are investigated and chemical and physical considerations for a lunar-derived soil are considered. It is noted that biological considerations for such a soil include controlled-environment crop production, both hydroponic and lunar regolith-based; microorganisms and the growth of higher plants in lunar-derived soils; and the role of microbes to condition lunar regolith for plant cultivation. Current research in the controlled ecological life support system (CELSS) project is presented in detail and future research areas, such as the growth of higher research plants in CELSS are considered. Optimum plant and microbiological considerations for lunar derived soils are examined.

Ming, Douglas W.↗
DOE OSTI2022

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirk) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

WA-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

IA-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗