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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Applications of Hyporheic Zone Sampling for Assessing VOC Plume Engineered Remediation and Natural Attenuation Effectiveness - 20414

Determining the efficacy of engineered remedial actions and/or natural attenuation as an acceptable EPA Record of Decision (ROD) must address long-term temporal and spatial variability. Since final plume downslope destinations are aquifers and related surface streams and rivers, hyporheic zone sampling is essential. Comprehensive hyporheic sampling documents plume groundwater remediation prior to upwelling into stream benthic strata and natural attenuation within this dynamic zone itself. Our intensive sampling of the Savannah River Site (SRS) Chemical, Metals, and Pesticides (CMP) Pits VOC plume-fringe from 2005 to 2018 documented PCE natural attenuation and effectiveness of In Situ Thermal Treatment (ISTT). Most plume hyporheic upwelling was delimited to a 20 m inflow reach along Pen Branch. Our study utilized corroborative sampling methodologies: ambient hole-water grab samples: passive diffusion bags (PDB); and hole-core sediment samples to confirm station to station spatial and temporal trends. VOC hot spot detections were confirmed from both groundwater and soil core samples. VOC pathways through the Pen Branch hyporheic zone were assessed at hole-installation using sequential soil samples from augered cores and grab-samples of hole-bottom water. Longer term, composite water samples were collected from PDBs deployed for a minimum two-week equilibration period. Soil samples were collected from the 15 and 65 cm core levels in December 2017 and June 2018 at six stations. Additional core depths of 40 and 85 cm were sampled in June 2018 at the highest VOC station (5DB80). All samples were analyzed in an EPA certified lab by purge and trap GC-MS. Effectiveness of previous ISTT and soil vapor extraction (SVE) for this CMP Pits PCE plume, was clearly documented by significant downward trends in VOC at hyporheic zone stations prior to December 2015. Achieving final stage conversions of PCE daughter products to ethene and CO{sub 2} may be limited depending upon suitable interactions between hyporheic zone sediment morphology, hydrology, and redox conditions. Because declines in VOC daughter products at our hyporheic stations may also be caused by physical actions of dilution and dispersion rather than true biochemical dechlorination, full quantification of natural attenuation requires the use of compound-specific isotope ratio analysis (CSIA) and microbial 16S rRNA with qPCR. To assist these next-phase efforts, a natural attenuation index (NAI) was used to help produce quicker, more cost-effective decision making for locating CSIA and microbial sampling efforts. The NAI used natural logarithm transformed GC-MS results for station VOC degradation compounds versus VOC parent compounds. Wide differences were observed between stations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1985

Interactions among sulfide-oxidizing bacteria

The responses of different phototrophic bacteria in a competitive experimental system are studied, one in which primary factors such as H2S or light limited photometabolism. Two different types of bacteria shared one limited source of sulfide under specific conditions of light. The selection of a purple and a green sulfur bacteria and the cyanobacterium was based on their physiological similarity and also on the fact that they occur together in microbial mats. They all share anoxygenic photosynthesis, and are thus probably part of an evolutionary continuum of phototrophic organisms that runs from, strictly anaerobic physiology to the ability of some cyanobacteria to shift between anoxygenic bacterial style photosynthesis and the oxygenic kind typical of eukaryotes.

Poplawski, R.↗
DOE OSTI2021

Soil minerals affect taxon-specific bacterial growth

Abstract Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages—particularly short-range order minerals—affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with 18O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25–36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Continental scale structuring of forest and soil diversity via functional traits

Trait-based ecology claims to offer a mechanistic approach for explaining the drivers that structure biological diversity and predicting the responses of species, trophic interactions and ecosystems to environmental change. However, support for this claim is lacking across broad taxonomic groups. A framework for defining ecosystem processes in terms of the functional traits of their constituent taxa across large spatial scales is needed. Here, we provide a comprehensive assessment of the linkages between climate, plant traits and soil microbial traits at many sites spanning a broad latitudinal temperature gradient from tropical to subalpine forests. Our results show that temperature drives coordinated shifts in most plant and soil bacterial traits but these relationships are not observed for most fungal traits. Shifts in plant traits are mechanistically associated with soil bacterial functional traits related to carbon (C), nitrogen (N) and phosphorus (P) cycling, indicating that microbial processes are tightly linked to variation in plant traits that influence rates of ecosystem decomposition and nutrient cycling. In conclusion, our results are consistent with hypotheses that diversity gradients reflect shifts in phenotypic optima signifying local temperature adaptation mediated by soil nutrient availability and metabolism. They underscore the importance of temperature in structuring the functional diversity of plants and soil microbes in forest ecosystems and how this is coupled to biogeochemical processes via functional traits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Synergistic Effects of a Chalkophore, Methanobactin, on Microbial Methylation of Mercury

Microbial production of the neurotoxin methylmercury (MeHg) is a significant health and environmental concern, as it can bioaccumulate and biomagnify in the food web. A chalkophore or a copper-binding compound, termed methanobactin (MB), has been shown to form strong complexes with mercury [as Hg(II)] and also enables some methanotrophs to degrade MeHg. It is unknown, however, if Hg(II) binding with MB can also impede Hg(II) methylation by other microbes. Contrary to expectations, MB produced by the methanotroph Methylosinus trichosporium OB3b (OB3b-MB) enhanced the rate and efficiency of Hg(II) methylation more than that observed with thiol compounds (such as cysteine) by the mercury-methylating bacteria Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. Compared to no-MB controls, OB3b-MB decreased the rates of Hg(II) sorption and internalization, but increased methylation by 5- to 7-fold, suggesting that Hg(II) complexation with OB3b-MB facilitated exchange and internal transfer of Hg(II) to the HgcAB proteins required for methylation. Conversely, addition of excess amounts of OB3b-MB or a different form of MB from Methylocystis strain SB2 (SB2-MB) inhibited Hg(II) methylation, likely due to greater binding of Hg(II). Collectively, our results underscore the complex roles of microbial exogenous metal-scavenging compounds in controlling net production and bioaccumulation of MeHg in the environment. Some anaerobic microorganisms convert inorganic mercury (Hg) into the neurotoxin methylmercury, which can bioaccumulate and biomagnify in the food web. While the genetic basis of microbial mercury methylation is known, factors that control net methylmercury production in the environment are still poorly understood. Here, it is shown that mercury methylation can be substantially enhanced by one form of an exogenous copper-binding compound (methanobactin) produced by some methanotrophs, but not by another. This novel finding illustrates that complex interactions exist between microbes and that these interactions can potentially affect the net production of methylmercury in situ .

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2010

Resilience of Alaska's Boreal Forest to Climatic Change

This paper assesses the resilience of Alaska s boreal forest system to rapid climatic change. Recent warming is associated with reduced growth of dominant tree species, plant disease and insect outbreaks, warming and thawing of permafrost, drying of lakes, increased wildfire extent, increased postfire recruitment of deciduous trees, and reduced safety of hunters traveling on river ice. These changes have modified key structural features, feedbacks, and interactions in the boreal forest, including reduced effects of upland permafrost on regional hydrology, expansion of boreal forest into tundra, and amplification of climate warming because of reduced albedo (shorter winter season) and carbon release from wildfires. Other temperature-sensitive processes for which no trends have been detected include composition of plant and microbial communities, long-term landscape-scale change in carbon stocks, stream discharge, mammalian population dynamics, and river access and subsistence opportunities for rural indigenous communities. Projections of continued warming suggest that Alaska s boreal forest will undergo significant functional and structural changes within the next few decades that are unprecedented in the last 6000 years. The impact of these social ecological changes will depend in part on the extent of landscape reorganization between uplands and lowlands and on policies regulating subsistence opportunities for rural communities.

Chapin, F. S., III↗
DOE OSTI2023

Interactions among soil texture, pore structure, and labile carbon influence soil carbon gains

Perennial vegetation with high plant diversity, e.g., restored prairie, is known for stimulation of soil carbon (C) gains, due in part to enhanced formation of pore structure beneficial for long-term C storage. However, the prevalence of this phenomenon across soils of different types remains poorly understood. The aim of the study was to assess the associations between pore structure, soil C, and their differences in monoculture switchgrass and polyculture restored prairie vegetation across a wide range of soils dominating the Upper Midwest of the USA. Six experimental sites were sampled, representing three soil types with texture ranging from sandy to silt loams. The two vegetation systems studied at each site were (i) monoculture switchgrass (Panicum virgatum L.), and (ii) polyculture restored prairie, also containing switchgrass as one of its species. X-ray computed micro-tomography (µCT) was employed to analyze soil pore structure. Structural equation modeling and multiple path analyses were used to assess direct and indirect effects of soil texture and pore characteristics on microbial biomass C (MBC), particulate organic matter (POM), dissolved organic C (DOC), short-term respiration (CO 2 ), and, ultimately, soil organic C (SOC). Across studied sites, prairie increased fractions of medium (50–150 µm Ø) pores by 11–45 %, SOC by 3–69 %, and MBC by 18–59 % (except for one site). The greater were the prairie-induced increases in the medium pore volumes, the greater were the prairie-induced SOC gains. Greater C losses via CO 2 and DOC contributed to slower C accumulation in the prairie soil. We surmise that the interactive feedback loop relating medium pores and soil C acts across a wide range of soil textures and is an important mechanism through which perennial vegetation with high plant diversity, such as restored prairie, promotes rapid SOC gains.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Altogether, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Epitaxial hexagonal boron nitride with high quantum efficiency

Two-dimensional (2D) hexagonal boron nitride (h-BN) is one of the few materials showing great promise for light emission in the far ultraviolet (UV)-C wavelength, which is more effective and safer in containing the transmission of microbial diseases than traditional UV light. In this report, we observed that h-BN, despite having an indirect energy bandgap, exhibits a remarkably high room-temperature quantum efficiency (~60%), which is orders of magnitude higher than that of other indirect bandgap material, and is enabled by strong excitonic effects and efficient exciton-phonon interactions. This study offers a new approach for the design and development of far UV-C optoelectronic devices as well as quantum photonic devices employing 2D semiconductor active regions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Editorial: Exogenous carbon-based materials in soil ecosystems

Various exogenous carbon-based materials (ECMs) such as crop straw, biochar, carbon-based nano-fertilizer, and microplastics have accumulated in soil ecosystems. These ECMs may cause direct and indirect impacts on soil properties, processes, productivity, and health, thus potentially changing the function and stability of soil ecosystems. However, large knowledge gaps still exist on ECMs in soil ecosystems, including their accumulation, interactions with soil components, and potential ecological impacts and risks. Therefore, more efforts are needed to further understand the impacts especially the long-term effects of ECMs in soil ecosystems. By generating new knowledge, this Research Topic aims to improve the understanding of the effects of ECMs on soil ecosystems, including soil quality, nutrient cycling, microbial ecology, crop growth, environmental health and ecological risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Interactions between molecular-scale processes and hyporheic exchange for understanding Fe-S-C cycling in riparian wetlands (Final Report)

Wetlands represent some of the most productive ecosystems on the planet and critically influence global environmental health. Specifically, wetlands promote water quality by transforming nutrients and organic compounds and sequestering metals and contaminants. Riparian wetland hyporheic zones, where toxic surface water and anoxic groundwater mix, exhibit dynamic conditions that drive steep redox gradients and promote hotspots of diverse and fluctuating microbial activity. Changes in climate, water quality, and water quantity can disturb hydrologic flow and biogeochemical processing in these environments. Understanding how sulfate loading, impacted by hydrologic flux and anthropogenic inputs, influences iron and carbon cycling in wetlands will be crucial for predicting water quality issues driven by iron mineral precipitation and sorption, such as the release of heavy metals and other toxic elements. We used a fully integrated multi-scale and multi-method approach to develop a mechanistic understanding of how hydrologic flow influences coupled iron and sulfur cycles in riparian wetlands. This entailed hydrological, geochemical, and microbial observations at two locations: an anthropogenic sulfate-impacted riparian wetland in northern Minnesota, and a low-sulfate Fe-rich riparian wetland in Tims Branch at the Savannah River Site (SRS). These sites were characterized by hydrologically dynamic conditions where the stream and wetland systems oscillated between gaining (upward flow) and losing (downward flow) conditions that recharged the system occasionally with oxidants that fueled a variety of biogeochemical reactions. Aqueous geochemical measurements of surface water, groundwater, and porewater samples were made alongside solid-phase geochemical analyses of sediment gravity cores. Bulk X-ray absorption spectroscopy at the Advanced Photon Source (APS; Argonne) interrogated the speciation and distribution of Fe and S mineral phases of the sediments. Interestingly, it was discovered that, despite strongly reducing conditions, Fe(III) compounds and a variety of intermediate valence S compounds were stable in the subsurface. Indeed, compounds like thiosulfate, S(0), and intermediate valence organosulfur compounds were more prevalent than FeS and pyrite. The composition of the sediments did change with changes in hydrologic flow, showing their reactivity in changing redox conditions. The abundance of these intermediate S compounds was likely formed as a result of anaerobic oxidation by aqueous and solid-phase Fe(III) compounds, fueling a cryptic S cycle that is driving the breakdown of organic matter in the hyporheic zone. Microbiome surveys showed a core community that seemed stable across the landscape, but changed with increasing depth into the sediment. The community composition did not seem to change dramatically with changes in season or hydrologic flow, except for some organisms that have the potential to contribute to S cycling. More work is needed to confirm their functional activity. These fine process-scale analyses were placed within a dynamic field context using physical flow parameters from surface water and groundwater level measurements. These data helped shed light on sulfur-driven biogeochemical processes in hydrologically dynamic riparian wetlands, addressing a gap in our understanding about the impacts of pollution and other anthropogenic changes on ecologically sensitive environments.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1990

Plants and their microbial assistants: Nature's answer to Earth's environmental pollution problems

The utilization of higher plants and their associated microorganisms to solve environmental pollution problems on Earth and in future space applications is briefly reviewed. If man is sealed inside closed facilities, he becomes a polluter of the environment. It is also common knowledge to most people that man cannot survive on Earth without green photosynthesizing plants and microorganisms. Therefore, it is vitally important to have a better understanding of the interactions of man with plants and microorganisms. Biosphere 2 and other related studies presently being conducted or planned, hopefully, will supply data that will help save planet Earth from impending environmental disaster. The development of means to utilize both air and water pollution as a nutrient source for growing green plants is examined.

Wolverton, B. C.↗
DOE OSTI2016

H 2 -saturation of high affinity H 2 -oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

Soil microbial communities are continuously exposed to H 2 diffusing into the soil from the atmosphere. N 2 -fixing nodules represent a peculiar microniche in soil where H 2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H 2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H 2 exposure from the atmosphere and N 2 -fixing nodules. Biphasic kinetic parameters governing H 2 oxidation activity in soil changed drastically upon elevated H 2 exposure, corresponding to a slight but significant decay of high affinity H 2 -oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H 2 . In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H 2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H 2 exposure, suggesting that H 2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H 2 -rich environments exert a direct influence on soil H 2 -oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Summary Biocrusts are phototroph‐driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth‐promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host–microbe co‐culture experiments between biocrust communities/biocrust isolates and a model grass ( Brachypodium distachyon ) or a dominant biocrust cyanobacterium ( Microcoleus vaginatus ), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates ( Bosea sp._L1B56, Pseudarthrobacter sp. _ L1D14 and Pseudarthrobacter picheli_ L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B . distachyon exudates, and supplementation of plant growth medium with this metabolite increased B . distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth‐promoting microbes and metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

59 BASIC BIOLOGICAL SCIENCES↗