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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH 4 ), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH 4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH 4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH 4 fluxes. CH 4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH 4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH 4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH 4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH 4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH 4 oxidation pathways in mitigating CH 4 emissions in Amazonian floodplains.

16S rRNA sequencing↗
DOE OSTI2024

Defined synthetic microbial communities colonize and benefit field-grown sorghum

The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, in this study, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2001

Culturability as an indicator of succession in microbial communities

Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to maintenance occurs with time. Results from this work indicate that the percentage of culturable cells may be a useful method for assessing the successional state of microbial communities.

NASA Center KSC↗
DOE OSTI2024

Rhizosphere microbial community structure in high-producing, low-input switchgrass families

Switchgrass ( Panicum virgatum L.) is a native, low-input North American perennial crop primarily grown for bioenergy, livestock forage, and industrial fiber. To achieve no-input switchgrass production that meets biomass needs, several switchgrass genotypes have been identified that have a low or negative response to nitrogen fertilizer, i . e ., the biomass accumulation with added nitrogen is less than or equal to that when grown without nitrogen. In order to improve the viability of low-input switchgrass production, a more detailed understanding of the biogeochemical mechanisms active in these select genotypes is needed. 16S and ITS amplicon sequencing and qPCR of key functional genes were applied to switchgrass rhizospheres to elucidate microbial community structure in high-producing, no-input switchgrass families. Rhizosphere microbial community structure differed strongly between sites, and nitrogen responsiveness.

Stonoha-Arther, Christina (ORCID:0000000263964507)↗
DOE OSTI2025

Old Woman Creek Wetland Sediment and Electrochemical Sensor Microbial Community, 2023

We are developing a technique to monitor microbiological activities referred to as zero resistance ammetry, which entails the deployment of graphite electrodes in sediments. Measurement of current between electrodes of contrasting redox regimes and/or predominant terminal electron accepting processes can be used as an indicator of the extents of microbiological activity. We deployed an electrode array at depths of 2 mm, 4 mm, 76 mm, 78 mm, 152 mm, 154 mm, 227 mm, and 229 mm below the wetland sediment water interface in the Old Woman Creek National Estuarine Research Center, Huron, OH, USA (Lat. = 41.380833, Long. = -82.508889). A core was collected from adjacent sediment and subsamples were collected from depth intervals of 0 – 25 mm, 25 – 127 mm, 127 – 128 mm, and below 178 mm. To determine if the microbial communities attached to the electrodes were reflective of the adjacent sediment-associated microbial community, we conducted a 16S rRNA gene-based (V4 region) survey of these respective materials. This data package contains the results of these surveys, including metadata on the depths from which samples were collected (samples.csv), DNA extraction and sequencing information (OWC_DEPTH_AMPLICON_SEQUENCING_METADATA), sequence processing information (OWC_DEPTH_BIOINFORMATIC_METADATA.csv), an operational taxonomic unit (OTU) table (OWC_DEPTH_97OTUS_TABLE.csv), and nucleotide sequences of OTUs (OWC_DEPTH_97OTUS_SEQS.fasta). All files can be opened using a text-editing application. The fasta file is compatible with bioinformatics applications.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1994

Microbial community structure at the U.S.-Joint Global Ocean Flux Study Station ALOHA: Inverse methods for estimating biochemical indicator ratios

Modeling biogeochemical fluxes in the marine plankton requires the application of factors for extrapolation of biomass indicators measured in the field (chlorophyll a, adenosine triphosphate, bacterial counts) to biomass carbon or nitrogen. These are often inferred from culture studies and are poorly constrained for natural populations. At least squares inverse method with a simple linear model constrains the values of several common indicator ratios, giving self-consistent solutions that provide useful information about the structure of the microbial community at our North Pacific Ocean study site (Station ALOHA (A Long-term Oligotrophic Habitat Assessment)). These results indicate that the fraction of the microbial biomass that is autotrophic (pigmented) is greater in the mixed layer than at the deep chlorophyll maximum layer and that heterotrophic bacteria are a significant but not necessarily predominant component of the microbial community in the euphotic zone.

Christian, James R.↗
NASA NTRS2004

Microbial astronauts: assembling microbial communities for advanced life support systems

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag.

Review↗
DOE OSTI2025

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2001

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

Jahnke, Linda L.↗
NASA NTRS1985

Microbial communities and microprofiles of sulfide and oxygen of alum rock sulfur springs

The microbial community of Alum Rock sulfur spring Site 3 was studied along one branch of the main stream and between the two branches, 150 cm distant from the source. The community at the source was dominated by green sulfur photosynthetic bacteria of the genus Chlorobium. At 15 cm to 35 cm from the source dominance in the community shifted to the genus Flexibacter at the surface of the mat and purple bacteria of the genus Chromatium underneath. At 50 cm to 80 cm colorless sulfur oxidizing bacteria of the genus Thiothrix began to appear. At 100 cm to 150 cm, the surface of the mat was still dominated by Flexibacter, but underneath dominance shifted to purple sulfur bacteria as above, as well as cyanobacteria of the genus Oscillatoria and Pseudonabaena. The measurements of temperature along the stream showed no significant gradient. Community variations appear to be controlled more by sulfide than temperature. Ten ml of the overlying water were taken and fixed immediately to determine the sulfide concentration by the methylene blue method. A sulfide concentration of 106 micro-m was calculated for the overlying water.

Fischer, U.↗
NASA NTRS2013

Characterization of Microbial Communities Found in Bioreactor Effluent

The purpose of this investigation was to examine microbial communities of simulated wastewater effluent from hollow fiber membrane bioreactors collected from the Space Life Science Laboratory and Texas Technical University. Microbes were characterized using quantitative polymerase chain reaction where a total count of bacteria and fungi were determined. The primers that were used to determine the total count of bacteria and fungi were targeted for 16S rDNA genes and the internal transcribed spacer, respectively. PCR products were detected with SYBR Green I fluorescent dye and a melting curve analysis was performed to identify unique melt profiles resulting from DNA sequence variations from each species of the community. Results from both the total bacteria and total fungi count assays showed that distinct populations were present in isolates from these bioreactors. This was exhibited by variation in the number of peaks observed on the melting curve analysis graph. Further analysis of these results using species-specific primers will shed light on exactly which microbes are present in these effluents. Information gained from this study will enable the design of a system that can efficiently monitor microbes that play a role in the biogeochemical cycling of nitrogen in wastewater on the International Space Station to assist in the design of a sustainable system capable of converting this nutrient.

Flowe, Candice↗
DOE OSTI2024

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in the Hamptons Road Sanitary District (HRSD) Biological Nutrient Removal Pilot Plant Operated with High and Low Dissolved Oxygen Conditions

In this study, we aimed to evaluate BNR and investigate microbial community changes when the DO is reduced in the aerated portions of wastewater treatment trains. We present a dataset of metagenomes obtained from activated sludge collected from the Hamptons Road Sanitary District treatment plant at the beginning of operation, when the DO was high, and at the end of operation, when the DO was low

dissolved oxgyen↗
DOE OSTI2024

Metatranscriptomes of California grassland soil microbial communities in response to rewetting

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought—providing a time series of short-term transcriptional response during rewetting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions

Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.

dissolved oxygen↗
DOE OSTI2024

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

Abstract Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

58 GEOSCIENCES↗
NASA NTRS1989

Distribution of inorganic species in two Antarctic cryptoendolithic microbial communities

Chemical differences were noted between two Antarctic cryptoendolithic (hidden within rock) microenvironments colonized by different microbial communities. Microenvironments dominated by cyanobacteria (BPC) had a higher pH (pH 7-8) than those dominated by lichen (LTL) (pH 4.5-5.5). In order to understand the interactions between the microbiota and the inorganic environment, the inorganic environment was characterized. Water-soluble, carbonate-bound, metal-oxide, organically bound, and residual inorganic species were sequentially extracted from rock samples by chemical means. Each fraction was then quantified using inductively coupled plasma atomic emission spectrometry. BPC contained much more water-soluble and carbonate-bound Ca and Mg than LTL. Metal-oxide species of Al, Fe, and Mn were more abundant in LTL than BPC. Metal oxides appeared to be mobilized (in the order Mn > Fe > Al) from the LTL lichen zone but remained immobile in BPC sandstone. The distribution of K and P bound to metal oxide reflected the distribution of iron oxide in LTL, an indication of the importance of iron in controlling the availability of nutrients in this ecosystem. Metal oxides in turn were likely controlled or influenced by organic matter associated with the lichen community. Despite overall depletion of Fe, Al, and K in the lichen zone, SEM X-ray analysis showed that they were enriched in fungal hyphae. Water-soluble P was present despite the presence of metal oxides, which sequester phosphate. This has biological relevance since P is an essential nutrient.

NASA Program Exobiology↗
DOE OSTI2024

Biogeochemical Responses and Microbial Community Dynamics Responding to Experimental Hydrogen Storage Conditions

Hydrogen has been identified as a flexible energy carrier with zero or negative carbon emission across multiple energy sectors. There is tremendous capacity for deep geologic storage of H2 but many aspects of feasibility, reliability, safety and the potential for unintended consequences need to be examined. As part of a larger programmatic effort to address the knowledge gaps, we aim to gain a better understanding of reservoir microbial communities and their metabolic and biogeochemical responses to hydrogen storage conditions. In this study we collected and characterized reservoir brine from candidate hydrogen storage sites in the southwestern U.S. for use in a temporal reactor series under blended storage conditions (40% H2, 40% CH4, 20% CO2) at reservoir temperature (60°C).

hydrogen storage↗