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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities

Abstract Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.

Environmental Sciences & Ecology↗
DOE OSTI2025

Microbial dispersal into surface soil is limited on a meter scale

Abstract Dispersal shapes microbial communities, yet it is largely unknown how fast or how far free-living microorganisms move in the environment. Here, we deployed microbial traps along transects spanning a grassland and neighboring shrubland to quantify the rate and distance at which microorganisms disperse into the soil surface. We found that bacteria disperse at a similar rate across the two ecosystems, and both bacteria and fungi exhibit a signature of dispersal limitation at a meter scale, indicating highly heterogeneous dispersal of microorganisms into soil.

Environmental Sciences & Ecology↗
DOE OSTI2024

Soil microenvironmental variation drives below‐ground trait variation and interacts with macroclimate to structure above‐ground trait variation of arctic shrubs

Abstract Intraspecific trait variation can influence plant performance in different environments and may thereby determine the ability of individual plants to respond to climate change. However, our understanding of its patterns and environmental drivers across different spatial scales is incomplete, especially in understudied regions like the Arctic. To fill this knowledge gap, we examined above‐ground and below‐ground traits from three shrub taxa expanding across the tundra biome and evaluated their relationships with multiple microenvironmental and macroclimatic factors. The traits reflected plant size and structure (plant height, leaf area and root to shoot ratio), leaf economics (specific leaf area, nitrogen content), and root economics and collaboration with mycorrhizal fungi (specific root length, root tissue density, nitrogen content, and ectomycorrhizal colonisation intensity). We also measured leaf and root δ 15 N and leaf δ 13 C to characterise nitrogen source and acquisition pathways and plant water stress. Traits were measured in replicated plots ( N = 135) varying in soil microclimate, thaw depth and organic layer thickness established across five sites spanning a macroclimate gradient in northern Alaska. This hierarchical design allowed us to disentangle the independent and combined effects of fine‐scale and broad‐scale factors on intraspecific trait variation. We found substantial intraspecific variation at fine spatial scales for most traits and less variation along the macroclimate gradient and between shrub taxa. Consistent with these patterns, microenvironmental factors, mainly soil moisture and thaw depth, interacted with macroclimate, mainly climatic water deficit, to structure size‐structural and leaf trait variation. In contrast, most root traits responded additively to thaw depth and macroclimate. Synthesis . Our results demonstrate that above‐ground and below‐ground tundra shrub traits respond differently to microenvironmental and macroclimatic variation. These differing responses contribute to substantial trait variation at fine spatial scales and may decouple above‐ground and below‐ground trait responses to climate change.

Environmental Sciences & Ecology↗
DOE OSTI2023

Prescribed fire selects for a pyrophilous soil sub‐community in a northern California mixed conifer forest

Abstract Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above‐ground response to fire has been well‐documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold‐change, while differentially abundant bacterial taxa generally had a negative fold‐change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub‐community composed of burn‐associated indicator taxa that were positively differentially abundant was enriched for non‐neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process‐driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.

Microbiology↗
DOE OSTI2023

High-affinity amide-lanthanide adsorption to gram-positive soil bacteria

The gram-positive soil bacterium, Arthrobacter nicotianae, uses multiple organic acid functional groups to adsorb lanthanides onto its cell surface. At relevant soil pH conditions of 4.0–6.0, many of these functional groups are de-protonated and available for cation sorption and metal immobilization. However, among the plethora of naturally occurring site types, A. nicotianae is shown to possess high-affinity amide and phosphate sites that disproportionately affect lanthanide adsorption to the cell wall. We quantify neodymium (Nd)-selective site types, reporting an amide-Nd stability constant of log 10 K = 6.41 ± 0.23 that is comparable to sorption via phosphate-based moieties. These sites are two to three orders of magnitude more selective for Nd than the adsorption of divalent metals to ubiquitous carboxyl-based moieties. This implies the importance of lanthanide biosorption in the context of metal transport in subsurface systems despite trace concentrations of lanthanides found in the natural environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil respiration spatial and temporal variability in China between 1961 and 2014

Soil respiration (Rs) plays an important role in terrestrial-atmospheric carbon exchange but remains one of the least studied components of the carbon cycle. How environmental changes influence Rs, and in turn, how Rs influences terrestrial carbon storage in China is unclear. Here, we estimated spatial patterns and temporal trends in Rs from 1961 to 2014 to determine the influence of the recent warming hiatus on the Rs temporal variability in China. We evaluated the relationship between Rs and a set of environmental factors and developed biome-specific Rs models that were parameterized based on 2,862 Rs records and 18 continuous variables (e.g., air temperature, precipitation and leaf area index). Based on the biome-specific Rs models and environmental information, we estimated the annual Rs as well as the change trend of Rs in China during the study period. The mean annual Rs from 1961 to 2014 was 3.50 (confidence interval +/- 0.87) Pg center dot C center dot year(-1). Rs in China increased at a rate of 0.008 Pg center dot C center dot year(-2) between 1982 and 1998 (warming period), but was static between 1999 and 2014 (warming hiatus). This reduction in Rs increase rate may have an important role in enhancing terrestrial carbon sequestration. These findings confirm that temporal heterogeneity in Rs could be influenced by regional environmental changes, and further help in improving the understanding of soil carbon dynamics in China.

Jian, Jinshi↗
DOE OSTI2024

Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum

Abstract Altering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk ( D ) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green ( dd ) sorghum but reduced carbon allocation in that of dry white ( DD ) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication

Plant-microbe interactions are mediated by signaling compounds that control vital plant functions, such as nodulation, defense, and allelopathy. While interruption of signaling is typically attributed to biological processes, potential abiotic controls remain less studied. Here, we show that higher organic carbon (OC) contents in soils repress flavonoid signals by up to 70%. Furthermore, the magnitude of repression is differentially dependent on the chemical structure of the signaling molecule, the availability of metal ions, and the source of the plant-derived OC. Up to 63% of the signaling repression occurs between dissolved OC and flavonoids rather than through flavonoid sorption to particulate OC. In plant experiments, OC interrupts the signaling between a legume and a nitrogen-fixing microbial symbiont, resulting in a 75% decrease in nodule formation. Our results suggest that soil OC decreases the lifetime of flavonoids underlying plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

ABSTRACT Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. IMPORTANCE Ecosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Biotechnology & Applied Microbiology↗
DOE OSTI2021

Enhancement of Nitrous Oxide Emissions in Soil Microbial Consortia via Copper Competition between Proteobacterial Methanotrophs and Denitrifiers

Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized, post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N 2 O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N 2 O production, with more pronounced responses observed for soils with lower copper content.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest Soil

Frankiaceae are bacterial endosymbionts that are also found free-living in soil. Here, we present the genome sequences of two novel bacterial members of the order Frankiales , class Actinobacteria , isolated from temperate terrestrial forest soils. The genomes for MT45 and GAS493 indicate a genetic capacity for carbohydrate degradation but not nitrogen fixation.

DeAngelis, Kristen M.↗
DOE OSTI2020

Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

ABSTRACT Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH 4 ). While sulfate loading from seawater intrusion may reduce CH 4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH 4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH 4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH 4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH 4 fluxes observed in oligohaline sediments. IMPORTANCE Low-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Near-Real-Time Forecast of Satellite-Based Soil Moisture Using Long Short-Term Memory with an Adaptive Data Integration Kernel

Nowcasts, or near-real-time (NRT) forecasts, of soil moisture based on the Soil Moisture Active and Passive (SMAP) mission could provide substantial value for a range of applications including hazards monitoring and agricultural planning. To provide such a NRT forecast with high fidelity, we enhanced a time series deep learning architecture, long short-term memory (LSTM), with a novel data integration (DI) kernel to assimilate the most recent SMAP observations as soon as they become available. The kernel is adaptive in that it can accommodate irregular observational schedules. Testing over the CONUS, this NRT forecast product showcases predictions with unprecedented accuracy when evaluated against subsequent SMAP retrievals. It showed smaller error than NRT forecasts reported in the literature, especially at longer forecast latency. The comparative advantage was due to LSTM’s structural improvements, as well as its ability to utilize more input variables and more training data. The DI-LSTM was compared to the original LSTM model that runs without data integration, referred to as the projection model here. We found that the DI procedure removed the autocorrelated effects of forcing errors and errors due to processes not represented in the inputs, for example, irrigation and floodplain/lake inundation, as well as mismatches due to unseen forcing conditions. The effects of this purely data-driven DI kernel are discussed for the first time in the geosciences. Furthermore, this work presents an upper-bound estimate for the random component of the SMAP retrieval error.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

Microbially induced calcium carbonate precipitation (MICP) holds potential for use in soil stabilization and carbon sequestration, with the overall efficiency of the process being a major determinant for use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such precipitation remain poorly characterized. To address this gap, we developed a four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Microbacterium sp., and Bacillus toyonensis), termed carbon storing consortium - A (CSC-A), that is capable of MICP. Prior work shows that MICP production is higher in CSC-A compared to the sum of carbonate produced by each member, suggesting carbonate production is driven by consortium dynamics. To that end we used a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of niche specialization by B. toyonensis and Microbacterium, while metatranscriptomic analysis suggests R. qingshengii is a keystone species during growth in urea. By comparing individual species’ metabolomes to the metabolic profile of a shared well of precipitated metabolites, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types to search the KEGG reactome highlighted a network centered around glutamine metabolism and branched chain amino acid biosynthesis under regulation during CSC-A growth in urea. Succinate metabolism was also a major node in this network and laboratory assays confirmed that increasing the amount of succinate in the growth medium leads to increased carbonate precipitation by CSC-A, a critical confirmation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortia to carbonate precipitation.

carbon storing consortium - A (CSC-A)↗
DOE OSTI2024

Data sets for Unraveling Iron Oxides as Abiotic Catalysts of Organic Phosphorus Recycling in Soil and Sediment Matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus species. The dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this hydrolytic cleavage. Limited evidence of this abiotic catalysis has relied on monitoring inorganic phosphate in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Experiments with various organic phosphorus compounds revealed up to 12-fold greater catalytic and adsorption reactivities with iron oxides than with the silicate and aluminosilicate minerals identified in the environmental samples. Remarkably, we obtained dephosphorylation rates by the iron oxides that are within reported enzymatic rates in soils. However, phosphorus cycle models do not yet include a quantitative account of the abiotic evolution of inorganic phosphate from organic phosphorus trapped on iron oxides in environmental matrices. Our findings imply a missing abiotic axiom for organic phosphorus mineralization in the phosphorus cycle.

54 ENVIRONMENTAL SCIENCES↗