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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Biological and medical sciences↗
DOE OSTI2025

Root and Leaf Traits of Alfalfa Exhibit Distinct Responses to Soil Microbial Communities and Environmental Stresses

Ongoing climate change is negatively impacting crop productivity globally. Past research has highlighted that a diverse soil microbial community and variation in plant traits for resource acquisition can mitigate the negative impacts of climate change factors on crop productivity. This study investigates the effects of two major environmental stressors—drought and salinity stress, on plant productivity, biomass allocation, and root and leaf trait responses under distinct soil microbial diversities. Our results showed that salinity stress had stronger negative impacts on plant productivity than drought stress. Shoot biomass decreased by 30% and 32.5% under drought and salinity stress, respectively, whereas the root biomass decreased by 32% only under salinity stress. Soil microbial diversity did not affect plant productivity. Next, root traits were mainly impacted by drought and salinity stress, whereas leaf traits were impacted by both environmental stresses and soil microbial diversity. Specific root length and specific root area decreased under drought, and root tissue density was minimal under salinity stress. Root traits were not affected by soil microbial communities. In contrast, the leaf nitrogen content increased, whereas pheophytin content (a breakdown product of chlorophyll) decreased when plants were grown in diverse microbial communities under environmental stresses, especially drought. These results highlight the importance of soil microbial diversity in impacting plant traits in response to environmental stresses. We showed that the soil microbial diversity influences both aboveground and belowground plant traits, indicating the need for better management practices to conserve and promote soil microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CarbStor: Development, Analysis and Modification of Carbon Storing Model Soil Communities

Soil microbial communities carry out a number of key processes including plant growth promotion, bioremediation and cycling of nutrients. Carbon cycling is among the most important of these nutrients that are metabolized and processed by the soil microbial community. Many of the carbon inputs are converted to alternative organic forms of carbon that can be used by plants or act as biomass for microbial growth. However, inorganic forms of carbon can also be produced by soil microbial communities including calcium carbonate (CaCO 3 ). Production of calcium carbonate is beneficial for the ecosystem in several ways: it can stabilize soils and improve soil health, especially denser soils with high clay content, it can act as a method of bioremediation, it can serve as an alternative carbon source for plants and it can be a way to store carbon in soil in a stable, inorganic manner for the long term. While the chemistry surrounding individual species carrying out this process is well known what is lacking is an understanding of how species interact in a community to drive carbonate production. As all microbial species in soil exist in a community setting gaining this knowledge is critical to our predicting and controlling this microbial phenotype to greatly improve soil health. The CarbStor project is focused on developing, analyzing and modifying defined microbial soil consortia that express phenotypes at both the species and community level to convert carbon into recalcitrant stable sources such as precipitated carbonate or microbial necromass. To take full advantage of the soil community for this process we will need to fill several key knowledge gaps (KG), three of which are the focus of CarbStor. KG1: Whether and to what degree microbial communities can be developed that produce precipitated carbon via microbial metabolism. KG2: What interspecies interactions drive the individual member phenotypes in defined communities that lead to carbon precipitation. KG3: How can these interactions be modified to enhance carbon sequestration beyond what native communities are capable of. We hypothesize that in a carbon sequestering community only a subset of species will express phenotypes related to carbon storage processes. We also hypothesize that these phenotypes are expressed as a result of interactions with other species in the community that are not involved in carbon storage processes and that these interactions can be harnessed to enhance community carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.

Winfrey, Claire C. [Department of Ecology and Evol↗
DOE OSTI2025

Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.

Active microbial community↗
DOE OSTI2026

Microbial community data from throughfall exclusion experiment: Metadata, SI, community composition, LefSe, and FunGuilR data tables from PARCHED Panama tropical forest soils, 2024-2025

Soil contains more carbon (C) than terrestrial vegetation and the atmosphere combined, with some of the largest terrestrial C stocks in tropical rainforests. Soil microbes decompose organic matter, playing a vital role in the storage or loss of soil C. With climate change, drought conditions are predicted to increase in many tropical regions, including both chronic drying and extended drought, potentially influencing these processes. This project explored the effects of chronic and seasonal drying on soil microbial communities across four distinct tropical forests in a long-term drying experiment. We investigated the effects of a chronic drying manipulation on soil microbial community abundance and variation across different forests and seasons. We also compared findings with previously published data from these forests after short-term drying. This project used soils from a long-term drying experiment established in 2018 across four seasonal lowland forests in Panama. Soils were collected from 0 – 10 cm depths during three seasonal periods in control and drying plots in 2024 and 2025 from a total of 32 plots (n = 4 per forest per treatment). The forests varied in baseline rainfall and soil fertility. We calculated alpha and beta diversity indices and compared taxonomic community composition. We found significant biogeographic variation in microbial diversity and taxonomy, with significant differences across the forests and significant effects of the drying treatment. Metadata and sample IDs are within Metadata_16S.csv and Metadata_ITS.csv. Relative abundance tables of every sample at every season are shown in the Excel workbooks 16S Relative Abundance.xlsx and ITS Relative Abundance.xlsx. They are then also shown in CSV files by each taxonomic level. Linear discriminant analysis effect size (LefSe) tables are shown for the full 16S and ITS datasets (n = 96), subsets for every site at every season (n = 8), and then for the forests with each plot merged by season (n = 8). FunGuildR data table of ITS data is uploaded.

Bacteria↗
NASA NTRS2022

Adaptation to environmental extremes structures functional traits in biological soil crust and hypolithic microbial communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semi-translucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities waging war using the Type VI Secretion System (T6SS) and hypoliths favoring diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

Biological soil crusts↗
DOE OSTI2025

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗
DOE OSTI2025

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils—however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18 O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils—which are often more water limited and pulse driven—have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

ABSTRACT The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

carbon and nitrogen cycles↗
DOE OSTI2024

Thermal Adaptation of Enzyme‐Mediated Processes Reduces Simulated Soil CO2 Fluxes Upon Soil Warming

Abstract Understanding factors influencing carbon effluxes from soils to the atmosphere is important in a world experiencing climatic change. Two important uncertainties related to soil organic carbon (SOC) stock responses to a changing climate are (a) whether soil microbial communities acclimate or adapt to changes in soil temperature and (b) how to represent this process in SOC models. To further explore these issues, we included thermal adaptation of enzyme‐mediated processes in a mechanistic SOC model (ReSOM) using the macromolecular rate theory. Thermal adaptation is defined here to encompass all potential responses of soil microbes and microbial communities following a change in temperature. To assess the effects of thermal adaptation of enzyme‐mediated processes on simulated SOC losses, ReSOM was applied to data collected from a 13‐year soil warming experiment. Results show that a model omitting thermal adaptation of enzyme‐mediated processes substantially overestimates observed CO 2 effluxes during the initial years of soil warming. The bias against observed CO 2 effluxes was lower for models including thermal adaptation of enzyme‐mediated processes. In addition, for a simulated linear 3°C soil warming over 100 years, models including thermal adaptation of enzyme‐mediated processes simulated SOC losses of a factor of three smaller than models omitting this process. As thermal adaptation of microbial community characteristics is generally not included in models simulating feedback between the soil, biosphere and atmosphere, we encourage future studies to assess the potential impact that microbial adaptation has on soil carbon – climate feedback representations in models. Plain Language Summary A major uncertainty in projecting how much soil organic carbon (SOC) will be converted to CO 2 as a consequence of climate change is related to how soil microbes may adapt to increasing soil temperatures. While this “microbial thermal adaptation” has been shown to occur in short‐term lab incubation experiments, its effect on SOC cycling on a decadal timescale is not clear. To address this knowledge gap, a mechanistic SOC model was used to simulate data collected from a 13‐year soil warming experiment, to assess how microbial thermal adaptation affects predicted SOC losses upon soil warming. The model results show that incorporating microbial thermal adaptation into the model led to reduced CO 2 effluxes from the soil to the atmosphere compared to the common approach of omitting this mechanism. Our results imply that projected SOC losses for the decades to come may be reduced when this mechanism is incorporated in land models. We therefore advocate for more research on the mechanisms controlling microbial thermal adaptation, and how to implement this mechanism in SOC models. Key Points A crucial aspect of soil organic carbon (SOC) models is the representation of soil microbes Predicted soil CO 2 fluxes upon soil warming are reduced when accounting for microbial thermal adaptation On a centennial time scale, this thermal adaptation results in up to a factor of three lower predicted SOC loss

Van de Broek, Marijn↗
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 OSTI2026

Switchgrass-associated soil microbes have subtle but distinct effects on germination vs. growth under drought

Soil microbial communities can play a large role in plant fitness, including plants’ response to drought. How microbes mediate drought response may also differ across the plants’ life stage, but studies rarely study causal effects of microbes on plant fitness at multiple stages. We conducted a greenhouse experiment on switchgrass (Panicum virgatum L.) to investigate how microbial presence (sterile bulk vs. live bulk soils) and microbial source (communities from bulk vs. rhizosphere soil) affect germination and seedling growth (life-stage) during drought. We also investigated how drought and life-stage alter the assembly of the inoculated communities. Both drought conditions and the absence of microbes reduced germination (49% and 50% fewer seedlings, respectively, p < 0.05), but there were few effects of microbial presence on older seedlings. In addition, microbial source had no effect on the evaluated plant traits, but interestingly, the initially similar bulk and rhizosphere communities became compositionally distinct after 34 days with germinating seeds, but not with seedlings. Therefore, it may be that the plants did respond to microbial source through changes in seed or root exudates, and calls for further study. Finally, while sometimes microbes did benefit plants under drought, we did not find evidence that they are especially beneficial in this condition. We suggest that microbes’ effects differ across plant life stage, and may be both positive and negative. Further research should advance understanding of plant stress tolerance within a framework of plant-microbiome co-development.

drought↗
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↗
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 OSTI2025

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

ABSTRACT Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15 N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15 N can be used to measure taxon-specific microbial N assimilation. Relative 15 N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15 N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches. IMPORTANCE Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15 N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15 N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Reed, Kinsey (ORCID:0000000155178664)↗