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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high–yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.

Yu, Ningning↗
DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Enhancing climate-smart crop performance in arid agrivoltaics systems: effects of photovoltaic shading and soil amendments on tepary bean growth, yield, and associated soil microbiome

As climate change expands the world’s arid and semiarid regions, sustainable systems that integrate food and energy production are becoming increasingly critical. Agrivoltaics—co-locating crops with photovoltaic (PV) panels—offers a dual land-use strategy that mitigates environmental stress by shading crops, conserving soil moisture, and enhancing PV efficiency. While climate-smart crops like the tepary bean ( Phaseolus acutifolius ) are well adapted to heat and drought, little is known about how these crops and their associated soil microbiomes respond to the unique microclimates created by PV shading. This study evaluated tepary bean performance and plant–microbial interactions under PV-shade vs. no shade across three soil amendment treatments at two experimental sites. We assessed plant traits including germination, phenology, biomass, height, as well as yield and bean morphology, alongside shifts in soil microbial composition and functional potential. Plants grown under PV-shade were generally taller, with extended reproductive periods and higher yields: 42% of shaded plants produced beans compared to only 8% under full sun. Shaded plants also produced rounder, higher-quality beans, whereas non-shaded plants yielded flatter, less developed beans. Microbial community composition was more strongly influenced by amendment and site conditions than by shading alone. Key microbial taxa (e.g., Glomeromycetes, Desulfobacterota ) and predicted functions (e.g., denitrification, nitrogen-respiration, sulfate reduction) were associated with differences in plant performance. Finally, combining agrivoltaic systems with targeted soil amendments can enhance crop yield and soil microbial functionality—offering a promising strategy for sustainable agriculture in arid landscapes.

14 SOLAR ENERGY↗
DOE OSTI2022

Influence of living grass Roots and endophytic fungal hyphae on soil hydraulic properties

Soil hydraulic properties are often estimated based on laboratory data or pedotransfer functions dependent on soil physical properties, which often do not consider potential impacts of soil roots or fungal hyphae. Here, we first review current knowledge of how these soil biotic components affect hydraulic properties, then we conducted laboratory experiments to specifically test if the presence of roots and mycorrhizal fungi had a significant effect on the hydraulic properties of two soils with contrasting textures: Flint sand and Hamblen silt loam. Soil cores were seeded with (Panicum virgatum) and grown in a greenhouse over three separate growth periods. The endophytic fungus Serendipita indica was injected as liquid inoculant into designated mycorrhizal cores. Saturated hydraulic conductivity (K sat ) measurements were made with a constant head permeameter, and soil water retention curves were obtained by the evaporation method, supplemented at the dry end for Hamblen silt loam with water activity meter data. Retention curve parameters were obtained by fitting the van Genuchten equation to the resulting measurements. Mean root volume ratios were higher in the mycorrhizal inoculated treatment than in the uninoculated treatment for both soils. For Flint sand, analysis of variance revealed that K sat was reduced by the presence of roots as compared to bare soil. This was likely due to roots clogging soil pores. Results also indicated the presence of roots changed the shape of the water retention curve for Flint sand by increasing water content at saturation and by reducing the slope of the curve. These changes suggested roots created additional porosity and broadened the pore-size distribution. The presence of mycorrhizal fungi accentuated the root effects. The influence of roots and mycorrhizal fungi on hydraulic properties was less obvious for the Hamblen silt loam, as none of the treatments differed from each other at p < 0.05. The results highlight the necessity to consider the impact of root and fungal structures on models of soil hydraulic properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Resistance, Resilience, and Recovery of Dryland Soil Bacterial Communities Across Multiple Disturbances

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge

Abstract Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.

Science & Technology - Other Topics↗
DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗
DOE OSTI2023

Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits

Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25–50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Land management effects on wet aggregate stability and carbon content

Land management affects soil structure and many other soil properties and processes. Our objectives were to evaluate soil organic C (SOC), aggregate size distribution, aggregate-associated C, and soil structure as affected by long-term land management and slope. A chronosequence of 38 on-farm sites with low to high (5–18%) slopes was selected to evaluate 5–40 yr of management. The sites were classified as business as usual (BAU) cropland (BAU-Crop), BAU pasture (BAU-Past), newly established conservation reserve program (CRP) areas (CRP-New), and established CRP (CRP-Old). Soil samples were collected from the 0-to-5- and 5-to-15-cm depth increments and processed for soil property measurements including fractionation by wet sieving into five aggregate size classes (>2,000, 1,000–2,000, 500–1,000, 250–500, and 53–250 μm). Within the surface 5 cm, mean weight diameter (MWD) and geometric mean diameter (GMD) were used to characterize soil structural stability. The BAU-Past and CRP-Old sites had 79% more macroaggregates (>2,000, 1,000–2,000, and 500–1,000 μm), 123% higher MWD, 38% higher GMD, and 47% higher SOC than BAU-Crop or CRP-New sites. The 5-to-15-cm depth increment showed a similar but lower magnitude response. Aggregate-associated C was quantified using a constant soil mass that reflected aggregate size distribution to prevent overestimating C content. Lower-slope locations had more SOC, more macroaggregates, more C associated with macroaggregates, and higher GMD and MWD compared with high-slope locations across all management classifications and soil depths. The results support our hypothesis that the high-slop soils may benefits from specific management decisions than the lower-sloping soils as a function of landscape property. We recommend reestablishing grassland on sloping land that is susceptible to excessive soil erosion, although those practices will likely take a long time to restore soil structural stability and SOC content to precultivation levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity

Background: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean type grassland administrated with 14 years of 7 g m –2 year –1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. Results: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. Conclusions: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The influence of alfalfa-switchgrass intercropping on microbial community structure and function

The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N 2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. Here we analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N 2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Switchgrass ( Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function

Abstract Switchgrass ( Panicum virgatum L.) production for biofuel has the potential to produce reasonable yields on lands not suited for conventional agriculture. We assessed nine switchgrass cultivars representing lowland and upland ecotypes grown for 11 years at a site in the upper Midwest USA for belowground differences in soil carbon and nitrogen stocks, soil organic matter fractions, and standing root biomass to 1 m depth. We also compared potential nitrogen mineralization and carbon substrate use through community‐level physiological profiling in surface soils (0–10 cm depth). Average yields and standing root biomass differed among cultivars and between ecotypes, but we found no significant cultivar‐related impacts on soil carbon and nitrogen stocks, on the distribution of particulate and mineral‐associated soil organic matter fractions, nor on potential nitrogen mineralization or microbial community‐level physiological profiles. That these traits did not differ among cultivars suggests that soil carbon and nitrogen gains under switchgrass are likely to be robust with respect to cultivar differences, and to this point not much affected by breeding efforts.

Agriculture↗
DOE OSTI2025

The role of soil chemical properties and microbial communities on Dendrocalamus brandisii bamboo shoot quality, Yunnan Province, China

Objective To explore the effects of soil nutrients and microbial communities on the quality of Dendrocalamus brandisii shoots in different regions, providing a scientific basis for their development and utilization. Methods Using seven different geographic sources of D. brandisii from Yunnan Province as research subjects, this study employs chemical analysis and high-throughput sequencing to reveal the relationship between soil nutrients, microbial functional groups, and the nutritional quality of bamboo shoots. Results The results indicate that there are significant differences in soil nutrient content among the regions ( p < 0.05), with bamboo shoots from Baoshan Changning (CN) exhibiting the best overall nutritional quality. The key factors influencing bacterial community changes include pH, available phosphorus (AP), and available potassium (AK). In contrast, the main factors affecting fungal community changes are pH, soil organic matter (SOM), available potassium (AK), and total nitrogen (TN). This version maintains clarity and logical flow, making it easier for readers to understand the different factors influencing bacterial and fungal community changes. The diversity indices of soil microbial communities among different sources of Dendrocalamus brandisii show significant differences ( p < 0.05). The dominant groups in the seven regions include Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Ascomycota, and Basidiomycota. The soil microbial community in Baoshan Changning (CN) shows significant structural differences compared to the other six regions, with the highest relative abundances of Chloroflexi and Acidobacteriota. In contrast, the highest relative abundance of Proteobacteria is found in Honghe Shiping (SP), while Actinobacteriota has the highest relative abundance in Yuxi Xinping (XP). RDA analysis indicates that soil nutrients (SOM, pH, AP, TN) affect the water content, soluble sugar, and crude fat of bamboo shoots. Additionally, the bacterial communities including Actinobacteriota, Chloroflexi, Patescibacteria, GAL15, and Cyanobacteria influence the water content, soluble sugar, ash content, protein, and lignin of bamboo shoots. Discussion In the fungal community, Basidiomycota, Kickxellomycota, Mucoromycota, unclassified-k-Fungi, and Glomeromycota affect the water content and tannin levels in bamboo shoots. In summary, soil nutrients and soil microorganisms are interconnected and work together to influence the quality of bamboo shoots.

Chen, Qian↗
DOE OSTI2021

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple spatiotemporal scales, from which macrosystem patterns in SOM emerge. Theory on SOM turnover recognizes the resulting spatial and temporal conditionality in the effect sizes of controls that play out across macrosystems, and couples them through evolutionary and community assembly processes. For example, climate history shapes plant functional traits, which in turn interact with contemporary climate to influence SOM dynamics. Selection and assembly also shape the functional traits of soil decomposer communities, but it is less clear how in turn these traits influence temporal macrosystem patterns in SOM turnover. Here, we review evidence that establishes the expectation that selection and assembly should generate decomposer communities across macrosystems that have distinct functional effects on SOM dynamics. Representation of this knowledge in soil biogeochemical models affects the magnitude and direction of projected SOM responses under global change. Yet there is high uncertainty and low confidence in these projections. To address these issues, we make the case that a coordinated set of empirical practices are required which necessitate (1) greater use of statistical approaches in biogeochemistry that are suited to causative inference; (2) long-term, macrosystem-scale, observational and experimental networks to reveal conditionality in effect sizes, and embedded correlation, in controls on SOM turnover; and (3) use of multiple measurement grains to capture local- and macroscale variation in controls and outcomes, to avoid obscuring causative understanding through data aggregation. Here, when employed together, along with process-based models to synthesize knowledge and guide further empirical work, we believe these practices will rapidly advance understanding of microbial controls on SOM and improve carbon cycle projections that guide policies on climate adaptation and mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗