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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Simulated nitrogen deposition and precipitation events alter microbial carbon cycling during early stages of litter decomposition

Plant litter decomposition is a major nutrient input to terrestrial ecosystems that is primarily driven by microorganisms. Litter quality is considered a key drive of decomposition; however, human-induced global disturbance like nitrogen deposition and increasing extreme precipitation events will shift nutrient availability during litter decomposition. Little is known about how shifting nutrient availability will impact dissolved organic matter concentrations and microbially driven carbon cycling that are critical to soil organic matter formation. This study investigated the effect of simulated nitrogen deposition and repeated precipitation events on microbially driven carbon flow during short-term litter decomposition using a ‘common garden’ experiment with microcosms containing sand and blue grama grass litter inoculated with different microbial communities. Overall, nitrogen deposition decoupled respiration and dissolved organic carbon (DOC) by increasing respiration and not affecting DOC concentrations. Moreover, nitrogen deposition had no effect on microbial carbon use efficiency (CUE). Repeated simulated precipitation events significantly increased DOC concentrations, decreased microbial CUE, increased the microbial metabolic quotient (qCO2), and altered microbial composition and diversity. These findings highlight the complex interactions and responses of surface litter decomposers to shifting nutrient availability and contradicts previous findings that nitrogen deposition will increase soil carbon sequestration from a larger supply of DOC and reduced respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Ant‐mediated ecosystem functions on a warmer planet: effects on soil movement, decomposition and nutrient cycling

Summary Direct and indirect consequences of global warming on ecosystem functions and processes mediated by invertebrates remain understudied but are likely to have major impacts on ecosystems in the future. Among animals, invertebrates are taxonomically diverse, responsive to temperature changes, and play major ecological roles which also respond to temperature changes. We used a mesocosm experiment to evaluate impacts of two warming treatments (+3·5 and +5 °C, set‐points) and the presence and absence of the ant Formica subsericea (a major mediator of processes in north temperate ecosystems) on decomposition rate, soil movement, soil respiration and nitrogen availability. Replicate 19‐L mesocosms were placed outdoors in lathe houses and continuously warmed for 30 days in 2011 and 85 days in 2012. Warming treatments mimicked expected temperature increases for future climates in eastern North America. In both years, the amount of soil displaced and soil respiration increased in the warming and ant presence treatments (soil movement: 73–119%; soil respiration: 37–48% relative to the control treatments without ants). Decomposition rate and nitrogen availability tended to decrease in the warmest treatments (decomposition rate: −26 to −30%; nitrate availability: −11 to −42%). Path analyses indicated that ants had significant short‐term direct and indirect effects on the studied ecosystem processes. These results suggest that ants may be moving more soil and building deeper nests to escape increasing temperatures, but warming may also influence their direct and indirect effects on soil ecosystem processes.

Del Toro, Israel↗
DOE OSTI2015

Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils

Abstract Lignin mineralization represents a critical flux in the terrestrial carbon (C) cycle, yet little is known about mechanisms and environmental factors controlling lignin breakdown in mineral soils. Hypoxia is thought to suppress lignin decomposition, yet potential effects of oxygen (O 2 ) variability in surface soils have not been explored. Here, we tested the impact of redox fluctuations on lignin breakdown in humid tropical forest soils during ten‐week laboratory incubations. We used synthetic lignins labeled with 13 C in either of two positions (aromatic methoxyl or propyl side chain C β ) to provide highly sensitive and specific measures of lignin mineralization seldom employed in soils. Four‐day redox fluctuations increased the percent contribution of methoxyl C to soil respiration relative to static aerobic conditions, and cumulative methoxyl‐C mineralization was statistically equivalent under static aerobic and fluctuating redox conditions despite lower soil respiration in the latter treatment. Contributions of the less labile lignin C β to soil respiration were equivalent in the static aerobic and fluctuating redox treatments during periods of O 2 exposure, and tended to decline during periods of O 2 limitation, resulting in lower cumulative C β mineralization in the fluctuating treatment relative to the static aerobic treatment. However, cumulative mineralization of both the C β ‐ and methoxyl‐labeled lignins nearly doubled in the fluctuating treatment relative to the static aerobic treatment when total lignin mineralization was normalized to total O 2 exposure. Oxygen fluctuations are thought to be suboptimal for canonical lignin‐degrading microorganisms. However, O 2 fluctuations drove substantial Fe reduction and oxidation, and reactive oxygen species generated during abiotic Fe oxidation might explain the elevated contribution of lignin to C mineralization. Iron redox cycling provides a potential mechanism for lignin depletion in soil organic matter. Couplings between soil moisture, redox fluctuations, and lignin breakdown provide a potential link between climate variability and the biochemical composition of soil organic matter.

Hall, Steven J.↗
DOE OSTI2020

Effects of nitrogen enrichment on tree carbon allocation: A global synthesis

Aim: Increased atmospheric nitrogen deposition may have profound effects on tree carbon allocation dynamics. However, a comprehensive understanding of how nitro-gen (N) enrichment influences carbon (C) allocation across plant functional processes and tree organs in individual trees remains elusive. Location: Global forest ecosystems. Time period: 1990–2018. Major taxa studied: Trees. Methods: We compiled data from 75 N addition experiments and conducted a meta-analysis to evaluate the responses of C source (photosynthesis), sinks (growth and respiration) and storage (non-structural carbohydrate concentrations) in different tree organs (foliage, above-ground wood and roots) to N enrichment. Results: N enrichment significantly enhanced C supply via photosynthesis (+39.6%, n = 128). C allocation to growth (biomass increment/production) significantly in-creased in foliage (+15.9%, n = 68) and above-ground wood (+31.8%, n = 64; bole, branch, stem and/or twig) with increasing N availability, but not in roots, whereas allocation increased in roots via increasing fine root turnover rate (+22.6%, n = 11). N fertilization significantly increased C allocation to respiration in above-ground wood (+46.6%, n = 12) and roots (+5.5%, n = 57), but not in foliage. N addition decreased non-structural carbohydrate (NSC) concentrations in foliage (-5.4%, n = 16) and roots (-5.0%, n = 21), but increased NSC in above-ground wood (+6.1%, n = 22). In addition, N enrichment effects were strongly affected by moderator variables. Main conclusions: Our results demonstrate that N addition increased C allocation to growth and respiration more strongly than C allocation to NSC storage, and increased C allocation to above-ground parts more strongly than to below-ground parts. Our results are useful for better understanding the response of tree functional processes at organ level to N enrichment. The existing data also reveal that more long-term ex-perimental studies on mature trees in tropical and boreal forests are urgently needed to provide a basis for forecasting tree responses to N enrichment at the global scale.

Li, Weibin↗
DOE OSTI2016

Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes

ABSTRACT NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides , an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethyl sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroides complex I enzymes (complex I A and complex I E ) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex I A ) or NADH oxidation (complex I E ). The canonical alphaproteobacterial complex I isozyme (complex I A ) was also shown to be important for routing electrons to nitrogenase-mediated H 2 production, while the horizontally acquired enzyme (complex I E ) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. IMPORTANCE Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides , a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated ( P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

yihuishen/metabolic_flux_regulation

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Shen, Yihui↗
DOE OSTI2024

yihuishen/T_cell_MFA

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Shen, Yihui↗
DOE OSTI2026

Data for Mitochondrial ATP Generation is More Proteome Efficient than Glycolysis

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Metabolomics↗
DOE OSTI2024

Data for Microbial-Explicit Processes and Refined Perennial Plant Traits Improve Modeled Ecosystem Carbon Dynamics

Globally, soils hold approximately half of ecosystem carbon and can serve as a source or sink depending on climate, vegetation, management, and disturbance regimes. Understanding how soil carbon dynamics are influenced by these factors is essential to evaluate proposed natural climate solutions and policy regarding net ecosystem carbon balance. Soil microbes play a key role in both carbon fluxes and stabilization. However, biogeochemical models often do not specifically address microbial-explicit processes. Here, we incorporated microbial-explicit processes into the DayCent biogeochemical model to better represent large perennial grasses and mechanisms of soil carbon formation and stabilization. We also take advantage of recent model improvements to better represent perennial grass structural complexity and life-history traits. Specifically, this study focuses on: 1) a plant sub-model that represents perennial phenology and more refined plant chemistry with downstream implications for soil organic matter (SOM) cycling though litter inputs, 2) live and dead soil microbe pools that influence routing of carbon to physically protected and unprotected pools, 3) Michaelis-Menten kinetics rather than first-order kinetics in the soil decomposition calculations, and 4) feedbacks between decomposition and live microbial pools. We evaluated the performance of the plant sub-model and two SOM cycling sub-models, Michaelis-Menten (MM) and first-order (FO), using observations of net ecosystem production, ecosystem respiration, soil respiration, microbial biomass, and soil carbon from long-term bioenergy research plots in the mid-western United States. The MM sub-model represented seasonal dynamics of soil carbon fluxes better than the FO sub-model which consistently overestimated winter soil respiration. While both SOM sub-models were similarly calibrated to total, physically protected, and physically unprotected soil carbon measurements, the models differed in future soil carbon response to disturbance and climate, most notably in the protected pools. Adding microbial-explicit mechanisms of soil processes to ecosystem models will improve model predictions of ecosystem carbon balances but more data and research are necessary to validate disturbance and climate change responses and soil pool allocation.

Field Data↗
DOE OSTI2021

Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus

Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Spatial Study 2022: Surface Water Samples, Cotton Strip Degradation, and Hydrologic Sensor Data across the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides data and photos generated from sample collection during the same one-week period at 48 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. The contents include surface water geochemistry data; river substrate grain size photos; stream depth data; manual chamber open channel respiration data; and field metadata (including qualitative information on instream and river corridor characteristics). Grain size photos can be used to improve estimates of channel substrate D50 data. The dataset also includes tensile strength and photos from cotton strip field degradation experiments; five-week sensor time series temperature, dissolved oxygen, pressure, pH, specific conductance, chlorophyll A, and turbidity data; plots of the sensor data; and R scripts used to generate the plots. Samples collected during this study were labeled as “Second Spatial Study” or “SSS.” A subset of data from the SSS samples were published in the contiguous United States (CONUS)-Scale Model-Sample (CM) study data package available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689 that presents data from across the CONUS. SSS data published in the CM data package were not included in this data package. They include dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), total nitrogen (TN), grain size, aerobic sediment respiration, dissolved oxygen (DO), and temperature. Parent IDs and Site IDs are consistent between the SSS and CM data packages, and they can be mapped directly so data across packages can be used together. Additionally, sensor data from a similar 2021 spatial study can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052 and 2021 sample data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1898914. The 2021 spatial study had some sites in common with this 2022 spatial study. This dataset is comprised of three photo folders and one main data folder with six subfolders. The photo folders contain photographs and videos of cotton strip retrieval and sediment quadrats. The main data folder consists of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) total suspended solids (TSS) data and cotton strip tensile strength data and averages; (5) field protocol; (6) readme; (7) methods codes; (8) international generic sample number (IGSN) mapping file; (9) sensor installation methods summary; (10) stream depth and averages; and (11) Ultrameter data and averages. The Sonar subfolder consists of Sonar time-series depth data and a processing script. The BarotrollAtm, DepthHOBO, MantaRiver, miniDOT, and miniDOTManualChamber subfolders contain time-series data, plots, and summary files. All files are .csv, .pdf, .txt, .R, .Rmd, .jpg, .jpeg, .AVI, .mp4, or .mov. The data package was originally published in April 2023. It was updated in August 2023 (v2; modified files) and September 2024 (v3; modified files). See the change history section in the readme for details. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Diurnal observations of basal stem CO2 efflux in three canopy dominant trees in the central Amazon

We explored mechanisms responsible for disturbance-induced shifts in carbon metabolism in forests north of Manaus, Brazil (S2º 38' 17", W60º 09' 25"), using data from a selective logging experiment (BIONTE). BIONTE (the BIOmass and NuTrient Experiment) selective logging treatments were initiated in the mid-1980s and comprised variable removal of commercial tree (not total) species basal area (T1 =32%, T2 = 42%, T3 = 69%), and control plots with no logging (T0). Raw data including tree base diameter (Db), CO2 concentration versus time inside a static stem chamber, and wood density were used to derive stem respiration rates (Rw), wood production rates (Pw), and wood carbon use efficiency (CUE). Changes in tree base diameter (Db; measured at 1.3 m height, or above the buttresses) was used to calculate wood production for individual trees (Pw). Wood density enabled calculation of stem growth rate in the same units as stem respiration (mmol C m-2 s-1). Four trees were randomly selected from five tree growth rate classes for each treatment block, for a total of 20 trees per treatment block, or 80 trees total from the BIONTE plots. Each of the 80 trees selected for the Rw study were outfitted with dendrometer bands (da Silva et al. 2002). Stem respiration was measured using the method described in Chambers et al. (2004). Briefly, an infra-red gas analyzer (LiCor 820) was operated as a closed dynamic chamber with a flow rate of 1.0 L min-1. Polyvinyl chloride (PVC) semi-cylindrical chambers (250–400 mL) were secured to the tree stem near the dendrometer bands using nylon straps. The measurement interval spanned 1–2 min, and the CO2 flux from the stem of each tree was quantified using the enclosed stem area and slope of the stem CO2 concentration versus time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Positive correlations between soil C stabilization and loss are regulated by roots, minerals, and microbes

Modern conceptual models of soil organic carbon (SOC) cycling place a strong focus on the microbe-mineral interactions that regulate C stabilization. However, the formation of ‘stable’ soil organic matter, which consists mainly of microbial residues bonded to mineral surfaces, is inextricably linked to C loss through microbial respiration. Therefore, what is the net impact of microbial metabolism on the total quantity of C held in the soil? To address this question, we constructed artificial root-soil systems to identify controls on C cycling across the plant-microbe-mineral continuum, simultaneously quantifying the formation of persistent mineral-associated C and C losses to respiration. Roots and minerals interacted to regulate these processes: while roots stimulated respiratory C losses and depleted mineral-associated C pools in low-activity clays, roots triggered formation of stable C in high-activity clays. Moreover, we observed a strong positive correlation between the formation of mineral-associated C and respiration. This suggests that the growth of persistent C pools which can resist subsequent disturbance comes at the expense of C loss from the system.

58 GEOSCIENCES↗
DOE OSTI2023

Scaling hyporheic nitrogen cycling in large river alluvial aquifers

Research Element 1: Denitrification is a difficult flux to measure when fluxes are low and when the ecosystem is difficult to sample. These attributes describe Nyack floodplain, a large gravel-bedded aquifer adjacent to the Middle Fork Flathead River. Given that denitrification is simply respiration with nitrate as a terminal electron acceptor, we reasoned that N 2 production should negatively covary with oxygen respiration so long that oxygen is available. We sampled 16 wells 8 times throughout a year and analyzed these water samples on a membrane-inlet mass spectrometer for N 2 :Ar and O 2 . We fit multilevel models to N 2 :Ar as a function of dissolved oxygen. Within wells, there was no relationship between O 2 and N 2 :Ar. Among wells N 2 :Ar increased as O 2 declined. Based on the slope of this relationship, ~ -0.07, and estimated oxygen respiration in Nyack derived from prior studies, a possible range for denitrification is 0-8 mmol m -2 d -1 corresponding to a turnover rate for nitrate of 0-0.2/d. This estimated turnover rate is in the lower 20% of rates measured in the LINX 2 study, yet shows that even in a low nitrate (0.005 mmol/L) aquifer denitrification can be a substantial sink for dissolved N. Research Element 3 and 4: We developed a new theoretical approach to describe the relationship between water inflow, water outflow, and water age in porous media control volumes under dynamic flow conditions. Our approach had three distinct steps. First we described the application of well-established equations borrowed from Chemical Engineering to describe water age distributions in the hyporheic zone under steady state conditions. We published the associated results in the scientific journal PLOS ONE. Second, we developed a new theory ("flow spans") to describe how predicted steady-state water age distributions will respond to time varying imbalances in hyporheic discharge and recharge. Finally, we developed a proof-of-concept simulation model based on the new theory and used the model to examine the effects of flow regulation on a simulated river with characteristics representative of western U.S. montane rivers with expansive hyporheic zones.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Removal of primary nutrient degrading members severely reduces growth of soil microbial communities even when additional degraders are present

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here we used a model substrate, chitin, and a Model Soil Consortium, MSC-2, to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this representative community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed as well as alterations in the metabolic profile, especially when Streptomyces was removed. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

McClure, Ryan S↗
DOE OSTI2023

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO 2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Biotechnological Applications of Microbial (Per)chlorate Reduction

While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries.

bio-souring control↗