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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Opportunities to advance the synthesis of ecology and evolution

Despite decades of research on the interactions between ecology and evolution, opportunities still remain to further integrate the two disciplines, especially when considering multispecies systems. Here, we discuss two such opportunities. First, the traditional emphasis on the distinction between evolutionary and ecological processes should be further relaxed as it is particularly unhelpful in the study of microbial communities, where the very notion of species is hard to define. Second, key processes of evolutionary theory such as adaptation should be exported to hierarchical levels higher than populations to make sense of biodiversity dynamics. Together, we argue that broadening our perspective of eco-evolutionary dynamics to be more inclusive of all biodiversity, both phylogenetically and hierarchically, will open up fertile new research directions and help us to address one of the major scientific challenges of our time, that is, to understand and predict changes in biodiversity in the face of rapid environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral‐associated organic matter

Summary Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two‐chamber microcosms where an air gap isolated AMF from roots, we 13 CO 2 ‐labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13 C enrichment. SOM density fractionation, 13 C NMR, and IRMS showed AMF transferred 0.77 mg C g −1 of soil (increasing total C by 2% relative to non‐mycorrhizal controls); 33% was found in occluded or mineral‐associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)‐enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF‐imported 13 C (> 20 atom%). Mapping sequences from 13 C‐SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13 C‐enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

13C SIP↗
DOE OSTI2024

Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Detection and Screening of Organic Contaminants in A Riverine System of Georgia Using Non-Targeted Analysis

Numerous organic chemicals exist within aquatic environments, yet effectively screening and prioritizing them is a huge challenge. This study provides a comprehensive investigation into the ecological dynamics of the North Oconee River within Athens-Clarke County, Georgia, with a specific focus on the distribution of 33 identified compounds, including a prominent pesticide. The research, conducted in the riverine ecosystems proximal to the Firefly trail, employs advanced analytical techniques to elucidate potential contamination sources arising from agricultural and urban runoff. Intriguingly, the study reveals North Oconee River near the Firefly Trail as a notable site for heightened pesticide contamination, warranting a meticulous exploration of its origins. Furthermore, the investigation unveils the intricate microbial degradation processes of malathion within the North Oconee River, elucidating the pivotal role played by microbial activity in river water. The detection of degradant byproducts prompts the considerations of bioavailability and toxicity, associating potential implications for the river’s overall ecological health. Ongoing research endeavors to precisely quantify environmental risks and unravel indigenous microbial degradation pathways, presenting pivotal contributions to the scientific community’s understanding of complex riverine ecosystems. This research serves as a foundational piece in informing sustainable environmental management practices and emphasizes the urgency of comprehensive stewardship in safeguarding aquatic ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

metagRoot: a comprehensive database of protein families associated with plant root microbiomes

The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.

Chasapi, Maria N↗
DOE OSTI2021

Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities

A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites

Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the “chassis” organism’s metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Characterization and Stimulation of Selenium Reducing Microbial Consortia from Real Flue Gas Desulfurization Wastewater Biological Treatment System

Selenium is released into the environment via anthropogenic activities such as coal combustion. The U.S. Environmental Protection Agency’s Effluent Limitation Guideline (ELG) Rule limits the release of selenium species into U.S. waterways. To meet the ELG limit for selenium, coal-fired power plants must treat the wastewater produced by the flue gas desulfurization (FGD) systems. Selenium removal is of interest because small changes of the concentrations of selenium in the environment can cause detrimental ecological consequences. Biological treatment is used to remediate this wastewater, but little is known about the individual species in the microbial consortium that reduce toxic water-soluble selenium oxyanions to insoluble elemental selenium. To optimize current biological treatment capabilities of this water, the selenium-reducing capabilities must be leveraged. In order to do so, the selenium-reducing bacteria (SeRB) in biological treatment systems must be characterized. This study will be the first to characterize the microbial consortia from a real FGD WW biological treatment system and provide insights on how to better achieve selenium removal via biological treatment. This work will provide insights into the microorganisms predominantly responsible for the reduction of selenium oxyanions in FGD wastewater biological treatment systems, which can be used to better optimize more efficient biological treatment strategies of this industrial waste.

geomicrobiology↗
DOE OSTI2021

Microbial diversity analysis of two full-scale seawater desalination treatment trains provides insights into detrimental biofilm formation

Detrimental biofilms on RO membranes remain a crucial challenge for seawater desalination. Comparative analysis of 16S rRNA gene amplicon sequencing data revealed differences and commonalities of biofilm communities associated with unit operations in the two largest seawater desalination facilities in the U.S., the Claude "Bud" Lewis Carlsbad Desalination Plant and the Tampa Bay Seater Desalination facility. At both plants, feedwater collected at a single time point was a poor indicator of the RO membrane communities, which showed far greater taxa diversity. The analysis of prefilter cartridges from the Carlsbad plant revealed similarly high taxon diversity as the RO module biofilms, with relevant differences. Algal sequences were enriched on the prefilter cartridges as were sequences representing Bdellovibrionota, which are predatory bacteria. Sequences representing opportunistic Gammaproteobacteria (i.e., Shewanella, Woesia) were present in significantly higher relative abundance on the RO membranes than in the prefilter cartridges, suggesting growth of certain taxa in the RO modules. Untargeted metabolomics distinguished intra- and inter-desalination plant biofilm samples, highlighting the potential value of this tool for biofilm monitoring. These findings underscore the value of omics tools for effective microbial monitoring, to understand biofouling dynamics within RO desalination plants, and to provide insight for the development of ecologically-informed biofilm control measures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits

We leverage the Kellogg Biological Station Long Term Ecological Research Main Cropping System Experiment (KBS MCSE) field experiment to test trade-offs among high growth yield (Y), resource acquisition (A), and stress tolerance (S) traits using metagenomic data from plots with different land use, drought manipulation, and C addition.

Jones, Jennifer M. [WK Kellogg Biological Station,↗
DOE OSTI2026

Linking Plant and Microbial Traits to Soil Carbon for Reliable and Resilient Bioenergy Systems

Bioenergy systems in the United States offer a dual opportunity to supply renewable feedstocks while enhancing ecosystem services such as hydrologic regulation, erosion control, and soil carbon (C) storage. National assessments highlight the potential to grow perennial energy crops to improve soil function and ecosystem resilience. Realizing this potential requires understanding the ecological mechanisms that govern how C is added, transformed, and stabilized in soils. Plant traits determine the quantity, depth, and chemistry of organic inputs, while microbial processes—including carbon use efficiency, necromass formation, and trophic interactions—mediate their transformation and partitioning among soil carbon pools. These biological pathways are shaped by soil physical and chemical properties, including aggregation, texture, and mineralogy, and by environmental drivers such as temperature, moisture, and disturbance, leading to context-dependent outcomes across landscapes. Management practices that diversify feedstocks, minimize disturbance, and maintain soil cover can promote both biomass production and C retention, while microbial amendments and rhizosphere engineering offer emerging, but often context-dependent, tools to optimize plant–microbe interactions. Trade-offs between biomass yield and soil carbon storage may arise when systems favor rapid aboveground productivity at the expense of belowground inputs and microbial processing, underscoring the importance of trait combinations that support both functions. Advances in monitoring, reporting, and verification—spanning precision agriculture, remote sensing, and biosensing—are improving predictive capacity through microbial-explicit process models and model–experiment (ModEx) frameworks. By connecting soil, plant, and microbial processes with advances in modeling and biosensing, this review outlines research priorities focused on trait-based parameterization and ModEx integration. These priorities will support the design of bioenergy systems that are both reliable and resilient, enhancing renewable energy production and ecosystem sustainability.

bioenergy systems↗
DOE OSTI2026

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.

Sorensen, Patrick O↗
DOE OSTI2021

Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration

Abstract Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene–microbe–environment interactions through the lens of enzyme kinetics.

Carlson, Hans K. (ORCID:0000000215835313)↗
DOE OSTI2026

From microbial diversity to functional potential using dimensionality reduction

The high dimensionality of microbial diversity data from ‘omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide ’omics informed ecotype diversity to leverage in mechanistic biogeochemical models.

Arctic Ocean↗
DOE OSTI2023

Plant–soil feedback under drought: does history shape the future?

Plant–soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant–microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting

Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying–rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying–rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (− exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.

drying-rewetting↗
DOE OSTI2022

Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau

Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 69 surface water and sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season associated with comparatively low and high antibiotic levels. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3?94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance and community composition of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. Further, we identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.

59 BASIC BIOLOGICAL SCIENCES↗