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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Background: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Results: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Conclusions: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

16S rRNA gene sequencing↗
DOE OSTI2020

Crewmember microbiome may influence microbial composition of ISS habitable surfaces

The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember’s microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember’s skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember’s microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew’s skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content

Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples. We then used high-throughput amplicon sequencing of the ITS and 16S rDNA regions to characterize these microbiomes. Leaf microbiomes were the least diverse and the most even in terms of OTU richness and abundance compared to near soil and far soil, especially in their bacterial component. Microbial composition was significantly and primarily affected by niche (leaves vs. soil) but also by soil management type and plant species in the fungal microbiome, while moisture content and pore sizes were more important drivers for the bacterial communities. The pore size effect was significantly dependent on moisture content, but only in the organic management type. Overall, our results refine our understanding of the decomposition of carbon residues in the soil and the factors that influence it, which are key for environmental sustainability and for evaluating changes in ecosystem functions.

16S rDNA↗
DOE OSTI2020

Drought Drives Spatial Variation in the Millet Root Microbiome

Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome

Abstract Due to the scarcity of organic matter (OM) sources in the bathypelagic (1000–4000 m depth), prokaryotic metabolism is believed to be concentrated on particles originating from the surface. However, the structure of active bathypelagic prokaryotic communities and how it changes across environmental gradients remains unexplored. Using a combination of 16S rRNA gene and transcripts sequencing, metagenomics, and substrate uptake potential measurements, here we aimed to explore how water masses aging and the quality of OM influence the structure of the active microbiome, and the potential implications for community function. We found that the relative contribution of taxa with a free‐living lifestyle to the active microbiome increased in older water masses that were enriched in recalcitrant OM, suggesting that these prokaryotes may also play a substantial role in the bathypelagic metabolism of vast areas of the ocean. In comparison to particle‐associated prokaryotes, free‐living prokaryotes exhibited lower potential metabolic rates, and harbored a limited number of two‐component sensory systems, suggesting they have less ability to sense and respond to environmental cues. In contrast, particle‐associated prokaryotes carried genes for particle colonization and carbohydrate utilization that were absent in prokaryotes with a free‐living lifestyle. Consistently, we observed that prokaryotic communities inhabiting older waters displayed reduced abilities to colonize particles, and higher capabilities to use complex carbon sources, compared to communities in waters with a higher proportion of labile OM. Our results provide evidence of regionalization of the bathypelagic active prokaryotic microbiome, unveiling a niche partitioning based on the quality of OM.

Marine & Freshwater Biology↗
DOE OSTI2021

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential

Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Abstract Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Larkin, Alyse A. (ORCID:0000000344660791)↗
DOE OSTI2026

Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes

Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with water-soluble monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC-preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC catabolic preferences may reflect the thermodynamic niche of microorganisms and we anticipate that extending research on microbial catabolic preferences to a greater variety of organic carbon substrates and diverse microbiomes will improve our understanding of microbial carbon cycling and trait evolution.

Hu, Ruiwen↗
DOE OSTI2021

Soil microbiome predictability increases with spatial and taxonomic scale

Soil microorganisms shape ecosystem function, yet it remains an open question whether we can predict the composition of the soil microbiome in places before observing it. Furthermore, it is unclear whether the predictability of microbial life exhibits taxonomic- and spatial-scale dependence, as it does for macrobiological communities. Here, we leverage multiple large-scale soil microbiome surveys to develop predictive models of bacterial and fungal community composition in soil, then test these models against independent soil microbial community surveys from across the continental United States. We find remark- able scale dependence in community predictability. The predictability of bacterial and fungal communities increases with the spatial scale of observation, and fungal predictability increases with taxonomic scale. These patterns suggest that there is an increasing importance of deterministic versus stochastic processes with scale, consistent with findings in plant and animal communities, suggesting a general scaling relationship across biology. Biogeochemical functional groups and high-level taxonomic groups of microorganisms were equally predictable, indicating that traits and taxonomy are both powerful lenses for understanding soil communities. Here, by focusing on out-of-sample prediction, these findings suggest an emerging generality in our understanding of the soil microbiome, and that this understanding is fundamentally scale dependent

Biogeography↗
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 OSTI2025

Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome

Camelina ( Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations, we grew camelina in the greenhouse using soil transplanted from 33 locations in the dryland wheat production area of eastern Washington. Bacterial, archaeal, and fungal communities from bulk soil, rhizosphere, and endosphere were characterized with 16S rRNA and internal transcribed spacer amplicon sequencing and were analyzed alongside site-specific climatic and edaphic data. We found that soil from the highest precipitation zone had higher alpha diversity than soil from the driest zone, but this effect was not seen in the greenhouse rhizosphere or endosphere. Plant compartment, cropping system zone, and soil origin all significantly influenced microbial composition, with soil pH and organic matter, as well as precipitation at origin, as major predictors. Analysis of abundance–occupancy distributions showed that the Actinobacteriota Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus in the rhizosphere were plant-selected, while the endosphere was characterized by a number of Actinobacteriota, Rhizobium, and Clostridium. Sphingomonas amplicon sequence variants were also consistently enriched in the rhizosphere, suggesting that they are present in soils collected throughout eastern Washington and may represent good candidate biostimulants. Several lignin decomposing fungi had site-specific rhizospheric distributions, suggesting that they may be dispersal-limited or result from the legacy effect of long-term wheat cropping. Overall, this study contributes to our understanding of microbiome assembly in and on camelina roots while also highlighting the potential impact of cropping history on soil- and plant-associated microbiomes. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Barnes, Elle M↗
DOE OSTI2020

Enhancement of microbiome management by machine learning for biological wastewater treatment

Here we propose to develop microbiome-based machine learning models to predict the response of biological wastewater treatment systems to environmental or operational disturbances or to design specific microbiomes to achieve a desired system function. These machine learning models can be used to enhance the stability of microbiome-based biological systems and warn against the failure of these systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth’s subsurface and surface environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont’s genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids

There is growing interest in producing beneficial products from wastes using microbiomes. We previously performed multiomic analyses of a bioreactor microbiome that converted carbohydrate-rich lignocellulosic residues to medium-chain carboxylic acids. Here, we present draft metagenome-assembled genomes from this microbiome, obtained from reactors in which xylose was the primary carbon source.

Scarborough, Matthew J.↗