105 results on '"Stahl, David"'
Search Results
2. Microbially mediated climate feedbacks from wetland ecosystems.
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Candry, Pieter, Abrahamson, Britt, Stahl, David Allan, and Winkler, Mari‐Karoliina Henriikka
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CLIMATE feedbacks ,WETLAND soils ,WETLANDS ,CLIMATE change models ,COASTAL wetlands ,ATMOSPHERIC models ,ECOSYSTEMS ,CARBON cycle - Abstract
Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%–30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale‐bridging framework guides the development of feedback loops describing how wetland‐specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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3. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.
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Goff, Jennifer L., Szink, Elizabeth G., Thorgersen, Michael P., Putt, Andrew D., Fan, Yupeng, Lui, Lauren M., Nielsen, Torben N., Hunt, Kristopher A., Michael, Jonathan P., Wang, Yajiao, Ning, Daliang, Fu, Ying, Van Nostrand, Joy D., Poole, Farris L., Chandonia, John‐Marc, Hazen, Terry C., Stahl, David A., Zhou, Jizhong, Arkin, Adam P., and Adams, Michael W. W.
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BACILLUS cereus ,MOBILE genetic elements ,GENOMICS ,CONTAMINATED sediments ,NITRATE reductase ,HEAVY metals ,GEOCHEMISTRY - Abstract
Bacillus cereus strain CPT56D‐587‐MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF‐matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%–40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species—largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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4. Microbial maintenance energy quantified and modeled with microcalorimetry.
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Hunt, Kristopher A., von Netzer, Frederick, Gorman‐Lewis, Drew, and Stahl, David A.
- Abstract
Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta‐analyses of data derived from chemostat studies. The model accurately predicted temperature‐dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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5. High increase in levels of lipoprotein(a) in plasma of patients with rheumatoid arthritis after COVID‐19.
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Stahl, David, Esser, Ruth L., Brück, Carolin, Thiele, Jan, Di Cristanziano, Veronica, Pesch, Carola tho, and Kofler, David M.
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LIPOPROTEINS , *STATISTICS , *C-reactive protein , *COVID-19 , *TIME , *RETROSPECTIVE studies , *RHEUMATOID arthritis , *DESCRIPTIVE statistics , *DATA analysis , *LIPIDS - Published
- 2023
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6. The influence of alfalfa‐switchgrass intercropping on microbial community structure and function.
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Cha, Gyuhyon, Meinhardt, Kelley A., Orellana, Luis H., Hatt, Janet K., Pannu, Manmeet W., Stahl, David A., and Konstantinidis, Konstantinos T.
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SWITCHGRASS ,CATCH crops ,INTERCROPPING ,MICROBIAL communities ,SYNTHETIC fertilizers ,AMMONIA-oxidizing bacteria ,ALFALFA - Abstract
Summary: The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2O, a potent greenhouse gas. Intercropping with nitrogen‐fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia‐oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia‐oxidizing bacteria abundance in fertilized plots significantly correlated to N2O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization. [ABSTRACT FROM AUTHOR]
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- 2021
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7. The path leading to the discovery of the ammoniaoxidizing archaea.
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Stahl, David A.
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RIBOSOMAL RNA , *METAGENOMICS , *BIOTIC communities , *HORIZONTAL gene transfer , *CARBON fixation - Published
- 2020
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8. Reply.
- Author
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Stahl, David and Kofler, David M.
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LIPOPROTEINS , *COVID-19 , *RHEUMATOID arthritis , *LIPIDS - Published
- 2023
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9. Nitrous oxide emissions associated with ammonia‐oxidizing bacteria abundance in fields of switchgrass with and without intercropped alfalfa.
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Pannu, Manmeet W., Meinhardt, Kelley A., Bertagnolli, Anthony, Fransen, Steven C., Stahl, David A., and Strand, Stuart E.
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SWITCHGRASS ,AMMONIA-oxidizing bacteria ,INTERCROPPING ,NITROUS oxide ,ALFALFA ,FERTILIZER application ,CELLULOSIC ethanol - Abstract
Summary: The nitrogen (N) fertilizer required to supply a bioenergy industry with sufficient feedstocks is associated with adverse environmental impacts, including loss of oxidized reactive nitrogen through leaching and the production of the greenhouse gas nitrous oxide (N2O). We examined effects on crop yield, N fate and the response of ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA) to conventional fertilizer application or intercropping with N‐fixing alfalfa, for N delivery to switchgrass (Panicum virgatum), a potential bioenergy crop. Replicated field plots in Prosser, WA, were sampled over two seasons for reactive nitrogen, N2O gas emissions, and bacterial and archaeal ammonia monooxygenase gene (amoA) counts. Intercropping with alfalfa (70:30, switchgrass:alfalfa) resulted in reduced dry matter yields compared to fertilized plots, but three times lower N2O fluxes (≤ 4 g N2O‐N ha−1 d−1) than fertilized plots (12.5 g N2O‐N ha−1 d−1). In the fertilized switchgrass plots, AOA abundance was greater than AOB abundance, but only AOB abundance was positively correlated with N2O emissions, implicating AOB as the major producer of N2O emissions. A life cycle analysis of N2O emissions suggested the greenhouse gas emissions from cellulosic ethanol produced from switchgrass intercropped with alfalfa cultivation would be 94% lower than emissions from equivalent gasoline usage. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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10. Iron‐ and aluminium‐induced depletion of molybdenum in acidic environments impedes the nitrogen cycle.
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Ge, Xiaoxuan, Vaccaro, Brian J., Thorgersen, Michael P., Poole, Farris L., Majumder, Erica L., Zane, Grant M., De León, Kara B., Lancaster, W. Andrew, Moon, Ji Won, Paradis, Charles J., von Netzer, Frederick, Stahl, David A., Adams, Paul D., Arkin, Adam P., Wall, Judy D., Hazen, Terry C., and Adams, Michael W. W.
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PSEUDOMONAS fluorescens ,MOLYBDENUM ,DENITRIFICATION ,NITRATE reductase ,GROUNDWATER - Abstract
Summary: Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO42−), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate‐contaminated acidic environment to investigate whether the formation of Fe‐ and Al‐precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co‐occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate‐induced Mo depletion. The depletion of naturally occurring Mo in nitrate‐ and Fe/Al‐contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial‐based nitrate reduction thereby extending the duration of nitrate in the environment. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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11. Ammonia‐oxidizing bacteria are the primary N2O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil.
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Meinhardt, Kelley A., Stopnisek, Nejc, Pannu, Manmeet W., Strand, Stuart E., Fransen, Steven C., Casciotti, Karen L., and Stahl, David A.
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AMMONIA-oxidizing bacteria ,ARCHAEBACTERIA ,MICROCOSM & macrocosm ,BIOMASS energy ,STATISTICAL correlation - Abstract
Summary: Most agricultural N
2 O emissions are a consequence of microbial transformations of nitrogen (N) fertilizer, and mitigating increases in N2 O emission will depend on identifying microbial sources and variables influencing their activities. Here, using controlled microcosm and field studies, we found that synthetic N addition in any tested amount stimulated the production of N2 O from ammonia‐oxidizing bacteria (AOB), but not archaea (AOA), from a bioenergy crop soil. The activities of these two populations were differentiated by N treatments, with abundance and activity of AOB increasing as nitrate and N2 O production increased. Moreover, as N2 O production increased, the isotopic composition of N2 O was consistent with an AOB source. Relative N2 O contributions by both populations were quantified using selective inhibitors and varying N availability. Complementary field analyses confirmed a positive correlation between N2 O flux and AOB abundance with N application. Collectively, our data indicate that AOB are the major N2 O producers, even with low N addition, and that better‐metered N application, complemented by selective inhibitors, could reduce projected N2 O emissions from agricultural soils. [ABSTRACT FROM AUTHOR]- Published
- 2018
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12. Constraint‐based modelling captures the metabolic versatility of <italic>Desulfovibrio vulgaris</italic>.
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Flowers, Jason J., Richards, Matthew A., Baliga, Nitin, Meyer, Birte, and Stahl, David A.
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DESULFOVIBRIO vulgaris ,OXIDATION-reduction reaction ,LACTATE dehydrogenase ,FERREDOXINS ,VITAMIN K2 ,SULFITES - Abstract
Summary: A refined
Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr‐Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027‐3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions ‐ three for sulfate respiration (with lactate, pyruvate or H2 /CO2 ‐acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr‐Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD+ in a flavin‐based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction. [ABSTRACT FROM AUTHOR]- Published
- 2018
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13. Relative impacts of light, temperature, and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean.
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Horak, Rachel E. A., Qin, Wei, Bertagnolli, Anthony D., Nelson, Alexa, Heal, Katherine R., Han, Hantten, Heller, Maija, Schauer, Andrew J., Jeffrey, Wade H., Armbrust, E. Virginia, Moffett, James W., Ingalls, Anitra E., Stahl, David A., and Devol, Allan H.
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AMMONIA analysis ,ANALYSIS of hydrogen peroxide ,PLANT photoinhibition ,SEA water analysis ,CYANOBACTERIA - Abstract
Abstract:
Thaumarchaeota are implicated as the major ammonia oxidizers in the ocean. However, the influence of various abiotic factors in determining their distribution and activity in the upper ocean remain largely unclear. Here, we examined the influence of light, hydrogen peroxide (H2 O2 ), and temperature on ammonia oxidation rates for communities dominated byThaumarchaeota at the nitrite maximum across two North Pacific transects. In situ ammonia oxidation was almost exclusively driven byThaumarchaeota , as inferred from ammonia monooxygenase subunit A (amoA ) genes,amoA transcripts, and inhibitor studies. A major shift in population structure near the eastern North Pacific Subtropical Front was revealed by sequence variation ofamoA genes, showing differentThaumarchaeota community structure in oligotrophic gyre and temperate regions. While the most dominant OTUs were closely related, we found significant differences in physiological responses to light and temperature of incubation. At four stations in different biogeochemical regimes, the impact of sunlight intensity and temperature on activity was evaluated using15 NH 4 +‐spiked whole seawater collected from the nitrite maximum and incubated at different depths on a free floating in situ array. Ammonia oxidation was usually completely inhibited by PAR at the surface and 21–45% inhibited at 1% surface PAR, whereas a temperature effect on ammonia oxidation was observed at only two of four stations. While inhibition due to H2 O2 cannot be ruled out in surface waters, our findings show that below the mixed layer, photoinhibition, and not H2 O2 toxicity, had a greater influence on ammonia oxidation. [ABSTRACT FROM AUTHOR]- Published
- 2018
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14. Robustness of a model microbial community emerges from population structure among single cells of a clonal population.
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Thompson, Anne W., Turkarslan, Serdar, Arens, Christina E., López García de Lomana, Adrián, Raman, Arjun V., Stahl, David A., and Baliga, Nitin S.
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MICROBIAL communities ,MICROORGANISM populations ,MICROBIAL ecology ,GENETIC regulation ,DESULFOVIBRIO vulgaris ,MICROORGANISMS - Abstract
Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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15. Influence of oxygen availability on the activities of ammonia-oxidizing archaea.
- Author
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Qin, Wei, Meinhardt, Kelley A., Moffett, James W., Devol, Allan H., Virginia Armbrust, E., Ingalls, Anitra E., and Stahl, David A.
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EFFECT of oxygen on bacteria ,AMMONIA-oxidizing archaebacteria ,MARINE bacteria geographical distribution ,NITROUS oxide & the environment ,GREENHOUSE gases & the environment ,OZONE layer depletion - Abstract
Recent studies point to the importance of oxygen (O
2 ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2 ), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations. We quantify the increasing N2 O production by marine AOA with decreasing O2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2 O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations. [ABSTRACT FROM AUTHOR]- Published
- 2017
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16. Mechanism for microbial population collapse in a fluctuating resource environment.
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Turkarslan, Serdar, Raman, Arjun V, Thompson, Anne W, Arens, Christina E, Gillespie, Mark A, Netzer, Frederick, Hillesland, Kristina L, Stolyar, Sergey, López García de Lomana, Adrian, Reiss, David J, Gorman‐Lewis, Drew, Zane, Grant M, Ranish, Jeffrey A, Wall, Judy D, Stahl, David A, and Baliga, Nitin S
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MICROORGANISM populations ,MICROBIAL growth ,DESULFOVIBRIO vulgaris ,METHANOCOCCUS maripaludis ,RNA sequencing ,PROTEOMICS ,MICROCALORIMETRY - Abstract
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts. Counterintuitively, the collapse phenomenon was prevented by a single regulatory mutation. We have characterized the mechanism for collapse by conducting RNA-seq analysis, proteomics, microcalorimetry, and single-cell transcriptome analysis. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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17. Agricultural land usage transforms nitrifier population ecology.
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Bertagnolli, Anthony D., McCalmont, Dylan, Meinhardt, Kelley A., Fransen, Steven C., Strand, Stuart, Brown, Sally, and Stahl, David A.
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NITROGEN fertilizers & the environment ,LAND use ,SOIL management ,AMMONIA-oxidizing archaebacteria ,NUCLEOTIDE sequence ,BIOMARKERS - Abstract
Application of nitrogen fertilizer has altered terrestrial ecosystems. Ammonia is nitrified by ammonia and nitrite-oxidizing microorganisms, converting ammonia to highly mobile nitrate, contributing to the loss of nitrogen, soil nutrients and production of detrimental nitrogen oxides. Mitigating these costs is of critical importance to a growing bioenergy industry. To resolve the impact of management on nitrifying populations, amplicon sequencing of markers associated with ammonia and nitrite-oxidizing taxa (ammonia monooxygenase- amo A, nitrite oxidoreductase- nxr B, respectively) was conducted from long-term managed and nearby native soils in Eastern Washington, USA. Native nitrifier population structure was altered profoundly by management. The native ammonia-oxidizing archaeal community (comprised primarily by N itrososphaera sister subclusters 1.1 and 2) was displaced by populations of N itrosopumilus, N itrosotalea and different assemblages of N itrososphaera (subcluster 1.1, and unassociated lineages of N itrososphaera). A displacement of ammonia-oxidizing bacterial taxa was associated with management, with native groups of Nitrosospira (cluster 2 related, cluster 3A.2) displaced by N itrosospira clusters 8B and 3A.1. A shift in nitrite-oxidizing bacteria ( NOB) was correlated with management, but distribution patterns could not be linked exclusively to management. Dominant nxrB sequences displayed only distant relationships to other NOB isolates and environmental clones. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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18. The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.
- Author
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Martens ‐ Habbena, Willm, Qin, Wei, Horak, Rachel E. A., Urakawa, Hidetoshi, Schauer, Andrew J., Moffett, James W., Armbrust, E. Virginia, Ingalls, Anitra E., Devol, Allan H., and Stahl, David A.
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AMMONIA-oxidizing bacteria ,NITRIC oxide ,OXIDATION of ammonia ,IMIDAZOLINES ,ARCHAEBACTERIA metabolism - Abstract
Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea ( AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria ( AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide ( NO) by N itrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide ( PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea ( ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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19. Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars.
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Bertagnolli, Anthony D., Meinhardt, Kelley A., Pannu, Manmeet, Brown, Sally, Strand, Stuart, Fransen, Steven C., and Stahl, David A.
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AMMONIA-oxidizing archaebacteria ,SOIL microbiology ,ENERGY crops ,GEOGRAPHICAL distribution of bacteria ,BACTERIAL diversity ,SOIL chemistry - Abstract
Ammonia-oxidizing thaumarcheota ( AOA) and ammonia-oxidizing bacteria ( AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene ( amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass ( P anicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. N itrosotalea-like and N itrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with N itrososphaera and N itrosospira cluster 3 A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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20. Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria.
- Author
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Meinhardt, Kelley A., Bertagnolli, Anthony, Pannu, Manmeet W., Strand, Stuart E., Brown, Sally L., and Stahl, David A.
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AMMONIA-oxidizing archaebacteria ,POLYMERASE chain reaction ,NITROGEN cycle ,AMMONIA monooxygenase ,GENETIC markers ,SOIL microbial ecology - Abstract
Ammonia-oxidizing archaea ( AOA) and bacteria ( AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase ( amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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21. Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography/tandem mass spectrometry.
- Author
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Heal, Katherine R., Carlson, Laura Truxal, Devol, Allan H., Armbrust, E. Virginia, Moffett, James W., Stahl, David A., and Ingalls, Anitra E.
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VITAMIN B complex ,SEAWATER ,LIQUID chromatography-mass spectrometry ,SOLID phase extraction - Abstract
RATIONALE Vitamin B
12 is an essential nutrient for more than half of surveyed marine algae species, but methods for directly measuring this important cofactor in seawater are limited. Current mass spectrometry methods do not quantify all forms of B12 , potentially missing a significant portion of the B12 pool. METHODS We present a method to measure vitamins B1 , B2 , B6 , B7 and four forms of B12 dissolved in seawater. The method entails solid-phase extraction, separation by ultra-performance liquid chromatography, and detection by triple-quadrupole tandem mass spectrometry using stable-isotope-labeled internal standards. We demonstrated the use of this method in the environment by analyzing B12 concentrations at different depths in the Hood Canal, part of the Puget Sound estuarine system in Washington State. RESULTS Recovery of vitamin B12 forms during the preconcentration steps was >71% and the limits of detection were <0.275 pM in seawater. Standard addition calibration curves in three different seawater matrices were used to determine analytical response and to quantify samples from the environment. Hydroxocobalamin was the main form of B12 in seawater at our field site. CONCLUSIONS We developed a method for quantifying four forms of B12 in seawater by liquid chromatography/mass spectrometry with the option of simultaneous analysis of vitamins B1 , B2 , B6 , and B7 . We validated the method and demonstrated its application in the field. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]- Published
- 2014
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22. The energy-conserving electron transfer system used by D esulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf.
- Author
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Meyer, Birte, Kuehl, Jennifer V., Price, Morgan N., Ray, Jayashree, Deutschbauer, Adam M., Arkin, Adam P., and Stahl, David A.
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ENERGY conservation ,CHARGE exchange ,DESULFOVIBRIO ,PYRUVATES ,FERMENTATION ,BISOPROLOL - Abstract
The adaptation capability of D esulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying D esulfovibrio alaskensis strain G20 under varying respiratory, fermentative and methanogenic coculture conditions in chemostats. Transition from lactate to pyruvate in coculture resulted in a dramatic shift in the population structure and closer interspecies cell-to-cell interactions. Lower methane production rates in coculture than predicted from pyruvate input was attributed to redirection of electron flow to fumarate reduction. Without a methanogenic partner, accumulation of H
2 and formate resulted in greater succinate production. Comparative transcript and gene fitness analysis in concert with physiological data of G20 wildtype and mutants demonstrated that pyruvate fermentation involves respiration of cytoplasmically formed fumarate using cytoplasmic and membrane-bound energy-conserving complexes, Rnf, Hdr-Flox-1 and Hmc. At the low H2 /formate levels maintained in coculture, Rnf likely functions as proton-pumping ferredoxin (Fd) : type-I cytochrome c oxidoreductase, which transitions to a proton-pumping Fdred : nicotinamide adenine dinucleotide ( NAD+ ) oxidoreductase at high H2 /formate levels during fermentation in monoculture. Hdr-Flox-1 is postulated to recycle Fdred via a flavin-based electron bifurcation involving NADH, Fdox and the thiol/disulphide-containing DsrC. In a menaquinone ( MQ)-based electron confurcation reaction, the high-molecular-weight cytochrome-c3 complex, Hmc, is proposed to then couple DsrCred and periplasmic H2 /formate oxidation using the MQ pool to fuel a membrane-bound fumarate reductase. [ABSTRACT FROM AUTHOR]- Published
- 2014
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23. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment.
- Author
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Amin, Shady A., Moffett, James W., Martens-Habbena, Willm, Jacquot, Jeremy E., Yang Han, Devol, Allan, Ingalls, Anitra E., Stahl, David A., and Armbrust, E. Virginia
- Subjects
AMMONIA ,NITRIFICATION ,NITROGEN compounds ,PARTICLES (Nuclear physics) ,NITRIFYING bacteria - Abstract
Ammonia oxidizing archaea (AOA) have recently been recognized as the primary nitrifiers in the marine environment; they thus play an important role in the nitrogen cycle. Available genome sequences of AOA indicate that numerous Cu-dependent enzymes are essential for both ammonia oxidation and electron transfer, suggesting a particularly high requirement for copper. However, our knowledge of the copper requirements of AOA and their response to copper limitation in the ocean is nonexistent. Here, we examine the copper requirements of the chemolithoautotrophic AOA Candidatus Nitrosopumilus maritimus SCM1 using a combination of the metal chelators ethylenediaminetetraacetic acid and 1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetraacetic acid and show that ammonia oxidation is limited at free cupric ion concentrations < 10
-12.7 mol L-1 , which are higher than concentrations frequently reported for many coastal and oceanic regimes. Prolonged exposure of cells to copper starvation for up to 6 d had no effect on the recovery of ammonia oxidation by N. maritimus. In addition, we present evidence that N. maritimus does not produce a copper-binding ligand (chalkophore) under copper limitation and therefore probably relies mainly on acquisition of copper ions from surrounding media. Copper limitation may be an important constraint on archaeal ammonia oxidation throughout the marine environment. [ABSTRACT FROM AUTHOR]- Published
- 2013
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24. Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons.
- Author
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Pelve, Erik A., Martens‐Habbena, Willm, Stahl, David A., and Bernander, Rolf
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DNA replication ,REPLICONS ,BIOMARKERS ,CHROMOSOMES ,BINDING sites ,HALOPHILIC microorganisms ,PHYSIOLOGY - Abstract
We report mapping of active replication origins in thaum- and euryarchaeal replicons using high-throughput sequencing-based marker frequency analysis. The chromosome of the thaumarchaeon Nitrosopumilus maritimus is shown to contain a single origin of replication, whereas the main chromosome in the halophilic euryarchaea Haloferax mediterranei and Haloferax volcanii each contains two origins. All replication origins specified bidirectional replication, and the two origins in the halophiles were initiated in synchrony. The p HM500 plasmid of H. mediterranei is shown to contain a single origin, and the copy numbers of five plasmid replicons in the two halophiles were inferred to be close to that of the main chromosome. Origin recognition boxes ( ORBs) that provide binding sites for Orc1/ Cdc6 replication initiator proteins are identified at all chromosomal origins, as well as in a range of additional thaumarchaeal species. An annotation update is provided for all three species. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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25. Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system.
- Author
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Yan, Jia, Haaijer, Suzanne C. M., Op den Camp, Huub J. M., Niftrik, Laura, Stahl, David A., Könneke, Martin, Rush, Darci, Sinninghe Damsté, Jaap S., Hu, Yong Y., and Jetten, Mike S. M.
- Subjects
ANAEROBIC bacteria ,AEROBIC bacteria ,AMMONIA-oxidizing bacteria ,BACTERIAL cultures ,TRANSMISSION electron microscopy ,BACTERIA morphology ,PHYSIOLOGICAL effects of oxygen - Abstract
In marine oxygen minimum zones ( OMZs), ammonia-oxidizing archaea ( AOA) rather than marine ammonia-oxidizing bacteria ( AOB) may provide nitrite to anaerobic ammonium-oxidizing (anammox) bacteria. Here we demonstrate the cooperation between marine anammox bacteria and nitrifiers in a laboratory-scale model system under oxygen limitation. A bioreactor containing ' Candidatus Scalindua profunda' marine anammox bacteria was supplemented with AOA ( Nitrosopumilus maritimus strain SCM1) cells and limited amounts of oxygen. In this way a stable mixed culture of AOA, and anammox bacteria was established within 200 days while also a substantial amount of endogenous AOB were enriched. ' Ca. Scalindua profunda' and putative AOB and AOA morphologies were visualized by transmission electron microscopy and a C
18 anammox [3]-ladderane fatty acid was highly abundant in the oxygen-limited culture. The rapid oxygen consumption by AOA and AOB ensured that anammox activity was not affected. High expression of AOA, AOB and anammox genes encoding for ammonium transport proteins was observed, likely caused by the increased competition for ammonium. The competition between AOA and AOB was found to be strongly related to the residual ammonium concentration based on amoA gene copy numbers. The abundance of archaeal amoA copy numbers increased markedly when the ammonium concentration was below 30 μM finally resulting in almost equal abundance of AOA and AOB amoA copy numbers. Massive parallel sequencing of mRNA and activity analyses further corroborated equal abundance of AOA and AOB. PTIO addition, inhibiting AOA activity, was employed to determine the relative contribution of AOB versus AOA to ammonium oxidation. The present study provides the first direct evidence for cooperation of archaeal ammonia oxidation with anammox bacteria by provision of nitrite and consumption of oxygen. [ABSTRACT FROM AUTHOR]- Published
- 2012
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26. Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus.
- Author
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Pelve, Erik A., Lindås, Ann-Christin, Martens-Habbena, Willm, de la Torre, José R., Stahl, David A., and Bernander, Rolf
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CELL division ,CELL cycle ,PROTEIN analysis ,CHROMOSOME replication ,CELL proliferation ,GENOMES - Abstract
Summary Cell division is mediated by different mechanisms in different evolutionary lineages. While bacteria and euryarchaea utilize an FtsZ-based mechanism, most crenarchaea divide using the Cdv system, related to the eukaryotic ESCRT-III machinery. Intriguingly, thaumarchaeal genomes encode both FtsZ and Cdv protein homologues, raising the question of their division mode. Here, we provide evidence indicating that Cdv is the primary division system in the thaumarchaeon Nitrosopumilus maritimus. We also show that the cell cycle is differently organized as compared to hyperthermophilic crenarchaea, with a longer pre-replication phase and a shorter post-replication stage. In particular, the time required for chromosome replication is remarkably extensive, 15-18 h, indicating a low replication rate. Further, replication did not continue to termination in a significant fraction of N. maritimus cell populations following substrate depletion. Both the low replication speed and the propensity for replication arrest are likely to represent adaptations to extremely oligotrophic environments. The results demonstrate that thaumarchaea, crenarchaea and euryarchaea display differences not only regarding phylogenetic affiliations and gene content, but also in fundamental cellular and physiological characteristics. The findings also have implications for evolutionary issues concerning the last archaeal common ancestor and the relationship between archaea and eukaryotes. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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27. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.
- Author
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Zhou, Aifen, He, Zhili, Redding-Johanson, Alyssa M., Mukhopadhyay, Aindrila, Hemme, Christopher L., Joachimiak, Marcin P., Luo, Feng, Deng, Ye, Bender, Kelly S., He, Qiang, Keasling, Jay D., Stahl, David A., Fields, Matthew W., Hazen, Terry C., Arkin, Adam P., Wall, Judy D., and Zhou, Jizhong
- Subjects
HYDROGEN peroxide ,OXIDATIVE stress ,DESULFOVIBRIO vulgaris ,BACTERIA ,SULFATES ,BACTERIAL genetics ,GENE expression - Abstract
Summary To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H
2 O2 -induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H2 O2 and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H2 O2 stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H2 O2 and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H2 O2 -induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H2 O2 stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H2 O2 -induced stresses. [ABSTRACT FROM AUTHOR]- Published
- 2010
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28. Diversity and host specificity of the Verminephrobacter–earthworm symbiosis.
- Author
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Lund, Marie B., Davidson, Seana K., Holmstrup, Martin, James, Sam, Kjeldsen, Kasper U., Stahl, David A., and Schramm, Andreas
- Subjects
EARTHWORMS ,SYMBIOSIS ,OLIGOCHAETA ,FLUORESCENCE in situ hybridization ,RNA polymerases - Abstract
Symbiotic bacteria of the genus Verminephrobacter ( Betaproteobacteria) were detected in the nephridia of 19 out of 23 investigated earthworm species ( Oligochaeta: Lumbricidae) by 16S rRNA gene sequence analysis and fluorescence in situ hybridization (FISH). While all four Lumbricus species and three out of five Aporrectodea species were densely colonized by a mono-species culture of Verminephrobacter, other earthworm species contained mixed bacterial populations with varying proportions of Verminephrobacter; four species did not contain Verminephrobacter at all. The Verminephrobacter symbionts could be grouped into earthworm species-specific sequence clusters based on their 16S rRNA and RNA polymerase subunit B ( rpoB) genes. Closely related host species harboured more closely related symbionts than did distantly related hosts. Co-diversification of the symbiotic partners could not be demonstrated unambiguously due to the poor resolution of the host phylogeny [based on histone H3 and cytochrome c oxidase subunit I (COI) gene sequence analyses]. However, there was a pattern of symbiont diversification within four groups of closely related hosts. The mean rate of symbiont 16S rRNA gene evolution was determined using a relaxed clock model, and the rate was calibrated with paleogeographical estimates of the time of origin of Lumbricid earthworms. The calibrated rates of symbiont 16S rRNA gene evolution are 0.012–0.026 substitutions per site per 50 million years and thus similar to rates reported from other symbiotic bacteria. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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29. Transmission of a bacterial consortium in Eisenia fetida egg capsules.
- Author
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Davidson, Seana K., Powell, Ryan J., and Stahl, David A.
- Subjects
EISENIA foetida ,EXCRETORY organs ,EGG cases (Zoology) ,EARTHWORMS ,MICROBACTERIACEAE - Abstract
The earthworm Eisenia fetida harbours Verminephrobacter eiseniae within their excretory nephridia. This symbiont is transferred from the parent into the egg capsules where the cells are acquired by the developing earthworm in a series of recruitment steps. Previous studies defined V. eiseniae as the most abundant cell type in the egg capsules, leaving approximately 30% of the bacteria unidentified and of unknown origin. The study presented here used terminal restriction fragment length polymorphism analysis together with cloning and sequencing of 16S rRNA genes to define the composition of the bacterial consortium in E. fetida egg capsules from early to late development. Newly formed capsules of E. fetida contained three bacterial types, a novel Microbacteriaceae member, a Flexibacteriaceae member and the previously described V. eiseniae. Fluorescent in situ hybridization (FISH) using specific and general rRNA probes demonstrated that the bacteria are abundant during early development, colonize the embryo and appear in the adult nephridia. As the capsules mature, Herbaspirillum spp. become abundant although they were not detected within the adult worm. These divergent taxa could serve distinct functions in both the adult earthworm and in the egg capsule to influence the competitive ability of earthworms within the soil community. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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30. Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis.
- Author
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Kalyuhznaya, Marina G., Martens-Habbena, Willm, Wang, Tiansong, Hackett, Murray, Stolyar, Sergey M., Stahl, David A., Lidstrom, Mary E., and Chistoserdova, Ludmila
- Subjects
METHANOL ,STABLE isotopes ,DENITRIFICATION ,LAKE sediments - Abstract
Summary In this work we assessed the potential for the denitrification linked to methanol consumption in a microbial community inhabiting the top layer of the sediment of a pristine lake, Lake Washington in Seattle. Stable isotope probing with
13 C methanol was implemented in near in situ conditions and also in the presence of added nitrate. This revealed that the bacterial population involved in methanol uptake was dominated by species belonging to the Methylophilaceae, most prominently species belonging to the genus Methylotenera. Based on relative abundance of specific phylotypes in DNA clone libraries generated from13 C labelled DNA, some of these species appear not to require nitrate to assimilate methanol while others assimilate methanol in a nitrate-dependent fashion. A pure culture of Methylotenera mobilis strain JLW8 previously isolated from the same study site was investigated for denitrification capability. This culture was demonstrated to be able to grow on methanol when nitrate was present, in aerobic conditions, while in media supplemented with ammonium it did not grow on methanol. The denitrifying capability of this strain was further demonstrated in defined laboratory conditions, by measuring accumulation of N2 O. This study provides new insights into the potential involvement of Methylophilaceae in global nitrogen cycling in natural environments and highlights the connection between global carbon and nitrogen cycles. [ABSTRACT FROM AUTHOR]- Published
- 2009
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31. Dietary Protein and Cellulose Effects on Chemical and Microbial Characteristics of Swine Feces and Stored Manure.
- Author
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Ziemer, Cherie J., Kerr, Brian J., Trabue, Steven L., Stahl, David A., and Davidson, Seana K.
- Subjects
SWINE nutrition ,LABORATORY swine ,ANIMAL droppings ,CELLULOSE ,MANURES ,SULFUR ,PHENOLS ,AMMONIA ,FATTY acids - Abstract
The article presents a study that investigates the effects of cellulose and dietary crude protein on the swine's manure and feces composition after diet feeding and storage for eight weeks. The pigs were fed twice a day wherein the urine and feces were gathered after feeding and were placed on manure storage containers. It reveals that the increased dietary cellulose on the eight week showed that feces have higher level of volatile fatty acids (VFA) and phenols. The study manifests that lower protein decreases phenolic concentrations, sulfur content and ammonia, while the dietary protein established the greatest effect on the chemical concentration of the manure. The results show that pigs did not completely adjusted with the diet after two weeks of giving the experimental diets.
- Published
- 2009
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32. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.
- Author
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Walker, Christopher B., Stolyar, Sergey, Chivian, Dylan, Pinel, Nicolas, Gabster, Jeffrey A., Dehal, Paramvir S., Zhili He, Zamin Koo Yang, Yen, Huei-Che B., Jizhong Zhou, Wall, Judy D., Hazen, Terry C., Arkin, Adam P., and Stahl, David A.
- Subjects
DESULFOVIBRIO vulgaris ,GENOMES ,LAKE sediments ,BIOSYNTHESIS ,SEDIMENTS - Abstract
The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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33. Elevated sulfate reduction in metal-contaminated freshwater lake sediments.
- Author
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Gough, Heidi L., Dahl, Amy L., Tribou, Erik, Noble, Peter A., Gaillard, Jean-François, and Stahl, David A.
- Published
- 2008
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34. Metal impacts on microbial biomass in the anoxic sediments of a contaminated lake.
- Author
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Gough, Heidi L., Dahl, Amy L., Nolan, Melissa A., Gaillard, Jean-François, and Stahl, David A.
- Published
- 2008
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35. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.
- Author
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de la Torre, José R., Walker, Christopher B., Ingalls, Anitra E., Könneke, Martin, and Stahl, David A.
- Subjects
AMMONIA ,ARCHAEBACTERIA ,NITROGEN cycle ,BIOGEOCHEMICAL cycles ,MEMBRANE lipids ,HOT springs ,NITRIFICATION ,NITROGEN compounds ,OXIDATION - Abstract
The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance. Their distribution appeared limited to low- and moderate-temperature environments until the recent finding of a diagnostic membrane lipid, crenarchaeol, in terrestrial hot springs. We report here the cultivation of a thermophilic nitrifier (‘ Candidatus Nitrosocaldus yellowstonii’), an autotrophic crenarchaeote growing up to 74°C by aerobic ammonia oxidation. The major core lipid of this archaeon growing at 72°C is crenarchaeol, providing the first direct evidence for its synthesis by a thermophile. These findings greatly extend the upper temperature limit of nitrification and document that the capacity for ammonia oxidation is broadly distributed among the Crenarchaeota. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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- View/download PDF
36. Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient.
- Author
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Bernhard, Anne E., Tucker, Jane, Giblin, Anne E., and Stahl, David A.
- Subjects
NITRIFICATION ,BACILLUS (Bacteria) ,AMMONIA ,OXIDATION ,MONOOXYGENASES ,POLYMERASE chain reaction - Abstract
The relationship between ammonia-oxidizing bacteria (AOB) and potential nitrification rates was examined along a salinity gradient in a New England estuary in spring and late summer over 3 years. Ammonia-oxidizing bacteria abundance was estimated by measuring gene copies of the ammonia monooxygenase catalytic subunit ( amoA) using real-time polymerase chain reaction. Ammonia-oxidizing bacteria abundance ranged from below detection to 6.0 × 10
7 amoA copies (gdw sediment)−1 . Mean potential nitrification rates ranged from 0.5 to 186.5 nmol N (gdw sediment)−1 day−1 . Both AOB abundance and potential rates were significantly higher in spring than late summer. Correlations between rates and abundance varied significantly among sites, but showed site-specific ammonia oxidation kinetics related to AOB community structure. The effect of salinity on potential nitrification rates was evaluated by incubating sediment from each site under four salinity conditions (0, 5, 10 and 30 psu). At all sites, rates were generally highest in the intermediate salinity treatments, but rates at the upstream site were inhibited at high salinity, while rates at the two downstream sites were inhibited at the lowest salinity. Although salinity appears to be an important factor in determining AOB distribution, it may not be the primary factor as AOB exhibited a broad range of salinity tolerance in our experiments. Our results indicate that there are significant differences in abundance and community composition of AOB along the salinity gradient, and the differences are reflected in community function. [ABSTRACT FROM AUTHOR]- Published
- 2007
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- View/download PDF
37. Saliva-Based Diagnostics Using 16S rRNA Microarrays and Microfluidics.
- Author
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STARKE, E. MICHELLE, SMOOT, JAMES C., WU, JER‐HORNG, LIU, WEN‐TSO, CHANDLER, DARRELL, and STAHL, DAVID A.
- Subjects
DENTAL caries ,DNA microarrays ,DIAGNOSIS ,PHYLOGENY ,SALIVA ,GENES - Abstract
The development of a diagnostic system based on DNA microarrays for rapid identification and enumeration of microbial species in the oral cavity is described. This system uses gel-based microarrays with immobilized probes designed within a phylogenetic framework that provides for comprehensive microbial monitoring. Understanding the community structure in the oral cavity is a necessary foundation on which to understand the breadth and depth of different microbial communities in the oral cavity and their role in acute and systemic disease. Our ultimate goal is to develop a diagnostic device to identify individuals at high risk for oral disease, and thereby reduce its prevalence and therefore the economic burden associated with treatment. This article discusses recent improvements of our system in reducing diffusional constraints in order to provide more rapid and accurate measurements of the microbial composition of saliva. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
38. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain.
- Author
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Walker, Christopher B., Stolyar, Sergey S., Pinel, Nic, Yen, Huei-Che B., Zhili He, Jizhong Zhou, Wall, Judy D., and Stahl, David A.
- Subjects
BACTERIOPHAGES ,DESULFOVIBRIO ,POLYMERASE chain reaction ,GRAM-negative bacteria ,DNA polymerases ,ELECTROPHORESIS ,GENOMES ,PHASE partition - Abstract
A novel sulfate-reducing bacterium (strain DePue) closely related to Desulfovibrio vulgaris ssp. vulgaris strain Hildenborough was isolated from the sediment of a heavy-metal impacted lake using established techniques. Although few physiological differences between strains DePue and Hildenborough were observed, pulse-field gel electrophoresis (PFGE) revealed a significant genome reduction in strain DePue. Comparative whole-genome microarray and polymerase chain reaction analyses demonstrated that the absence of genes annotated in the Hildenborough genome as phage or phage-related contributed to the significant genome reduction in strain DePue. Two morphotypically distinct temperate bacteriophage from strain Hildenborough were recovered using strain DePue as a host for plaque isolation. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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- View/download PDF
39. Impact of prehybridization PCR amplification on microarray detection of nitrifying bacteria in wastewater treatment plant samples.
- Author
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Siripong, Slil, Kelly, John J., Stahl, David A., and Rittmann, Bruce E.
- Subjects
NUCLEIC acid probes ,NITRIFYING bacteria ,WASTEWATER treatment ,SEWAGE disposal plants ,RNA - Abstract
A gel-based microarray that included a set of 26 oligonucleotide probes targeting all nitrifying bacteria at varying levels of specificity suggested the presence of targeted microorganisms when hybridized to RNA isolated from a wastewater treatment plant, but could not discriminate between perfectly matched and mismatched sequences due in part to low signal intensity. To enhance sensitivity and improve discrimination, polymerase chain reaction was used to selectively amplify the 16S rRNA genes of specific nitrifier groups. RNA transcribed from these DNA templates was hybridized to the microarray and thermal dissociation analysis was used to characterize the specificity of hybridization. Amplification with Nitrospira-specific primers resulted in the selective amplification of this target group, confirmed by both a significant increase in signal intensity and a melting profile identical to the reference RNA. In contrast, Nitrobacter was not detected in the environmental samples with probe Nbac1000 despite pre-amplification with Nitrobacter-specific primers, indicating the absence of strains containing this Nitrobacter-specific sequence. Pre-amplification using primers specific for β-Proteobacterial ammonia-oxidizing bacteria resulted in a significant increase in signal intensity for probe Nso190, but melting profiles for probe Nso190 showed a slight deviation between amplified RNA and the reference microorganism, suggesting that the amplification products contained some sequences that varied by a single nucleotide difference in the probe target region. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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- View/download PDF
40. Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system.
- Author
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Bernhard, Anne E., Donn, Thomas, Giblin, Anne E., and Stahl, David A.
- Subjects
BACTERIA ,SALINITY ,ESTUARIES ,RIVERS ,NITROGEN compounds ,NITROGEN cycle ,BIOGEOCHEMICAL cycles - Abstract
Ammonia-oxidizing bacteria (AOB) play an important role in nitrogen cycling in estuaries, but little is known about AOB diversity, distribution and activity in relation to the chemical and physical changes encountered in estuary systems. Although estuarine salinity gradients are well recognized to influence microbial community structure, few studies have examined the influence of varying salinity on the diversity and stability of AOB populations. To investigate these relationships, we collected sediment samples from low-, mid- and high-salinity sites in Plum Island Sound estuary, MA, during spring and late summer over 3 years. Ammonia-oxidizing bacteria distribution and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) analysis of the ammonia monooxygenase ( amoA) gene, and fragments were identified by screening amoA clone libraries constructed from each site. Most striking was the stability and low diversity of the AOB community at the high-salinity site, showing little variability over 3 years. Ammonia-oxidizing bacteria at the high-salinity site were not closely related to any cultured AOB, but were most similar to Nitrosospira spp. Ammonia-oxidizing bacteria at the mid- and low-salinity sites were distributed among Nitrosospira-like sequences and sequences related to Nitrosomonas ureae/oligotropha and Nitrosomonas sp. Nm143. Our study suggests that salinity is a strong environmental control on AOB diversity and distribution in this estuary. [ABSTRACT FROM AUTHOR]
- Published
- 2005
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- View/download PDF
41. Hydrothermal vent gastropods from the same family (Provannidae) harbourℇ- andγ-proteobacterial endosymbionts.
- Author
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Urakawa, Hidetoshi, Dubilier, Nicole, Fujiwara, Yoshihiro, Cunningham, Dale E., Kojima, Shigeaki, and Stahl, David A.
- Subjects
HYDROTHERMAL vents ,GASTROPODA ,SUBMARINE topography ,IN situ hybridization ,SYMBIOSIS ,RNA - Abstract
The discovery of new hydrothermal vent systems in the back-arc basins of the Western Pacific revealed chemosynthesis-based faunal communities distinct from those of other vents. These vents are dominated by two related gastropods ( Alviniconcha spp. and Ifremeria nautilei) that harbour symbiotic bacteria in their gills. We used comparative 16S ribosomal RNA (rRNA) gene sequencing and in situ hybridization with rRNA-targeted probes to characterize the bacterial symbionts of Alviniconcha sp. and I. nautilei from the Manus Basin in the Western Pacific. The analyses revealed that these two gastropod species, although affiliated with the same family, harbour phylogenetically distant chemosymbionts, suggesting independent origins of these endosymbioses. The I. nautilei endosymbiont clusters with sulfur-oxidizing bacteria within theγ-Proteobacteria, as is the case for all previously characterized endosymbionts from a wide diversity of host taxa harbouring thioautotrophic prokaryotes. In contrast, the Alviniconcha endosymbiont is affiliated with sulfur-oxidizing bacteria within theℇ-Proteobacteria. These results show that bacteria from theℇ-Proteobacteria are also capable of forming endosymbiotic associations with marine invertebrates from chemosynthetic environments. More generally, the endosymbiotic lifestyle is now shown to be distributed throughout all recognized classes of the Proteobacteria. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
42. Pathways of organic carbon oxidation in a deep lacustrine sediment, Lake Michigan.
- Author
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Thomsen, Uffe, Thamdrup, Bo, Stahl, David A., and Canfield, Donald E.
- Subjects
SIDEROPHORES ,ORGANIC compounds ,OXIDATION ,BIOMINERALIZATION ,INORGANIC compounds ,DENITRIFYING bacteria - Abstract
Rates of microbial iron reduction and other pathways of organic carbon (C
org ) oxidation were investigated in sediment from a 100-m deep site in Lake Michigan. Total benthic mineralization rates of 6.8 and 8.0 mmol m-2 d-1 , respectively, were determined from benthic flux measurements and by summation of dissolved inorganic carbon (ΣCO2 ) accumulation rates measured in anoxic incubations of sediment in discrete depth intervals to 18 cm depth. Carbon oxidation rates were highest near the sediment surface and decreased asymptotically toward zero. A Corg half-life of 0.06 yr was estimated in the oxic zone, but the half-life increased by more than two orders of magnitude in the deep anoxic layers. Mineralization in the oxic zone (0-2.1 cm) accounted for 37% of the total ΣCO2 production, whereas microbial iron reduction was the most important pathway of carbon oxidation, accounting for 44%; sulfate reduction accounted for 19%, and methanogenesis was negligible. Denitrification accounted for <3% of Corg oxidation. Sulfate reduction was suppressed in the upper 5 cm, where oxygen, manganese, and iron reduction prevailed. Below this zone, sulfate reduction peaked but coexisted with microbial iron reduction. All Mn reduction was apparently coupled to iron and sulfide oxidation in the upper 6 cm. Below that level, a transient accumulation of iron monosulfide and pyrite implied that sulfate reduction increased during the 19th century because of anthropogenic atmospheric sulfur deposition. Sediment mixing through bioturbation was crucial for the cycling of Mn, Fe, and S, and estimates of biodiffusion coefficients were 0.02-0.3 cm² d-1 . [ABSTRACT FROM AUTHOR]- Published
- 2004
- Full Text
- View/download PDF
43. Acidovorax -like symbionts in the nephridia of earthworms.
- Author
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Schramm, Andreas, Davidson, Seana K., Dodsworth, Jeremy A., Drake, Harold L., Stahl, David A., and Dubilier, Nicole
- Subjects
MICROORGANISMS ,BIODEGRADATION ,FLUORESCENCE in situ hybridization ,NITROGEN - Abstract
Summary Dense accumulations of bacteria in the excretory organs, nephridia, were first described more than 75 years ago in members of the annelid family Lumbricidae (earthworms). These nephridial symbionts were assumed to play a role in the degradation of proteins in the excretory fluid for nitrogen recycling. In the present study, the phylogenetic affiliation of the nephridial bacteria of the earthworms Lumbricus terrestris , Aporrectodea tuberculata , Octolasion lacteum and Eisenia foetida was resolved. The 16S rRNA gene sequences of the symbionts formed a monophyletic cluster within the genus Acidovorax . Similarity between symbiont sequences from different host species was 95.5–97.6%, whereas similarity was> 99% between symbiont sequences from individuals of the same species. Densely packed bacteria were detected in the ampulla of the nephridia by fluorescence in situ hybridization (FISH) using Acidovorax -specific oligonucleotide probes. No other bacterial cells could be found by FISH, although a few sequences other than Acidovorax had been found by PCR and cloning. These results suggest that the Acidovorax- earthworm symbiosis is a stable, host-specific association that has evolved from a common bacterial ancestor. Given the close phylogenetic relationship of the symbionts to proteolytic, free-living Acidovorax species, they may indeed play a role in protein degradation during nitrogen excretion by earthworms. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
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44. Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State.
- Author
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Baker, Brett J., Moser, Duane P., MacGregor, Barbara J., Fishbain, Susan, Wagner, Michael, Fry, Norman K., Jackson, Brad, Speolstra, Nico, Loos, Steffen, Takai, Ken, Lollar, Barbara Sherwood, Fredrickson, Jim, Balkwill, David, Onstott, Tullis C., Wimpee, Charles F., and Stahl, David A.
- Subjects
BACTERIA ,BOREHOLE mining ,BASALT ,GRAM-positive bacteria - Abstract
Summary We characterized the diversity of sulphate-reducing bacteria (SRB) associated with South African gold mine boreholes and deep aquifer systems in Washington State, USA. Sterile cartridges filled with crushed country rock were installed on two hydrologically isolated and chemically distinct sites at depths of 3.2 and 2.7 km below the land surface (kmbls) to allow development of biofilms. Enrichments of sulphate-reducing chemolithotrophic (H
2 ) and organotrophic (lactate) bacteria were established from each site under both meso- and thermophilic conditions. Dissimilatory sulphite reductase (Dsr) and 16S ribosomal RNA (rRNA) genes amplified from DNA extracted from the cartridges were most closely related to the Gram-positive species Desulfotomaculum thermosapovorans and Desulfotomaculum geothermicum , or affiliated with a novel deeply branching clade. The dsr sequences recovered from the Washington State deep aquifer systems affiliated closely with the South African sequences, suggesting that Gram-positive sulphate-reducing bacteria are widely distributed in the deep subsurface. [ABSTRACT FROM AUTHOR]- Published
- 2003
- Full Text
- View/download PDF
45. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries.
- Author
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Schramm, Andreas, Fuchs, Bernhard M., Nielsen, Jeppe L., Tonolla, Mauro, and Stahl, David A.
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RNA ,MOLECULAR cloning ,GENE libraries ,FLUORESCENCE in situ hybridization - Abstract
Summary A method is presented for fluorescence in situ hybridization (FISH) of 16S rRNA gene clones targeting in vivo transcribed plasmid inserts (Clone-FISH). Several different cloning approaches and treatments to generate target-rRNA in the clones were compared. Highest signal intensities of Clone-FISH were obtained using plasmids with a T7 RNA polymerase promoter and host cells with an IPTG-inducible T7 RNA polymerase. Combined IPTG-induction and chloramphenicol treatment of those clones resulted in FISH signals up to 2.8-fold higher than signals of FISH with probe EUB338 to cells of Escherichia coli . Probe dissociation curves for three oligonucleotide probes were compared for reference cells containing native (FISH) or cloned (Clone-FISH) target sequences. Melting behaviour and calculated T
d values were virtually identical for clones and cells, providing a format to use 16S rRNA gene clones instead of pure cultures for probe validation and optimization of hybridization conditions. The optimized Clone-FISH protocol was also used to screen an environmental clone library for insert sequences of interest. In this application format, 13 out of 82 clones examined were identified to contain sulphate-reducing bacterial rRNA genes. In summary, Clone-FISH is a simple and fast technique, compatible with a wide variety of cloning vectors and hosts, that should have general utility for probe validation and screening of clone libraries. [ABSTRACT FROM AUTHOR]- Published
- 2002
- Full Text
- View/download PDF
46. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach.
- Author
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Liu, Wen-Tso, Mirzabekov, Andrei D., and Stahl, David A.
- Subjects
OLIGONUCLEOTIDES ,MICROBIOLOGY - Abstract
SummaryThe utility of a high-density oligonucleotide microarray (microchip) for identifying strains of five closely related bacilli (Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus medusa and Bacillus subtilis) was demonstrated using an approach that compares the non-equilibrium dissociation rates (‘melting curves’) of all probe–target duplexes simultaneously. For this study, a hierarchical set of 30 oligonucleotide probes targeting the 16S ribosomal RNA of these bacilli at multiple levels of specificity (approximate taxonomic ranks of domain, kingdom, order, genus and species) was designed and immobilized in a high-density matrix of gel pads on a glass slide. Reproducible melting curves for probes with different levels of specificity were obtained using an optimized salt concentration. Clear discrimination between perfect match (PM) and mismatch (MM) duplexes was achieved. By normalizing the signals to an internal standard (a universal probe), a more than twofold discrimination (> 2.4×) was achieved between PM and 1-MM duplexes at the dissociation temperature at which 50% of the probe–target duplexes remained intact. This provided excellent differentiation among representatives of different Bacillus species, both individually and in mixtures of two or three. The overall pattern of hybridization derived from this hierarchical probe set also provided a clear ‘chip fingerprint’ for each of these closely related Bacillus species. [ABSTRACT FROM AUTHOR]
- Published
- 2001
- Full Text
- View/download PDF
47. Evidence for tight coupling between active bacteria and particulate organic carbon during seasonal stratification of Lake Michigan.
- Author
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Van Mooy, Benjamin, MacGregor, Barbara, Hollander, David, Nealson, Ken, and Stahl, David
- Published
- 2001
- Full Text
- View/download PDF
48. Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the....
- Author
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MacGregor, Barbara J., van Mooy, Benjamin, Baker, Brett J., Mellon, Mark, Moisander, Pia H., Paerl, Hans W., Zehr, Jonathan, Hollander, David, and Stahl, David A.
- Subjects
MICROBIOLOGY ,NITROGEN fixation - Abstract
Examines the microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Significance of atmospheric N[sub 2] on the lake; Role of bacteria in the nitrogen fixation; Extent of nitrogen fixation competence during stratified season.
- Published
- 2001
- Full Text
- View/download PDF
49. Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes.
- Author
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Ziemer, Cherie J., Sharp, Richard, Stern, Marshall D., Cotta, Michael A., Whitehead, Terence R., and Stahl, David A.
- Subjects
MICROORGANISM populations ,MICROBIAL ecology ,BIOLOGICAL adaptation - Abstract
A model rumen system, dual-flow continuous culture fermenters, was evaluated by two comparative criteria in two experiments using ribosomal (r)RNA-targeted DNA probes to compare key microbial groups in samples. The initial experiment measured temporal changes in population structure during adaptation of ruminal microbial populations in fermenters over 240 h. The fermenter inoculum contained 34.9% Bacteria, 60.1% Eukarya and 6.8% Archaea measured as a fraction of total small subunit (SSU) rRNA quantified using a universal probe. The cellulolytic bacterial genus Fibrobacter comprised 9.5% of total SSU rRNA in the inoculum. After 240 h of fermenter operation, the average abundance was 80.9% Bacteria, 6.1% Eukarya, 5.1% Archaea and Fibrobacter genus accounted for 6.6% of the total SSU rRNA. Divergence between ruminal and fermenter population structure was evaluated in the second experiment and samples were classified as ruminal, inoculum or fermenter (96, 120, 144 and 168 h of fermenter operation). Fermenter samples had higher relative abundances of Bacteria (84.5%) and Archaea (2.1%) and lower relative abundances of Eukarya (1.8%) than ruminal samples (average 48.0% Bacteria, 1.3% Archaea and 61.5% Eukarya). The relative abundance of Fibrobacter was similar in all samples, averaging 2.5%. The ruminal and fermenter samples had similar proportions of F. succinogenes and F. succinogenes subgroup 3 (as a percentage of Fibrobacter SSU rRNA). Fibrobacter succinogenes subgroup 1 and F. intestinalis proportions of Fibrobacter were lower in fermenter samples (8.2% and 0.7% respectively) than in ruminal samples (28.4% and 2.2% respectively). Fermenters were able to maintain a core prokaryotic community structure similar to the native microbial community in the rumen. Although protozoa populations were lost, maintenance of Fibrobacter and archaeal populations indicated that the model system supported a functional community structure similar to the rumen. This model rumen... [ABSTRACT FROM AUTHOR]
- Published
- 2000
- Full Text
- View/download PDF
50. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment.
- Author
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Sahm, Kerstin, MacGregor, Barbara J., Jørgensen, Bo B., and Stahl, David A.
- Subjects
BACTERIAL genetics ,NUCLEIC acid hybridization ,MARINE sediment microbiology - Abstract
In the past, enumeration of sulphate-reducing bacteria (SRB) by cultivation-based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot-blot hybridization is a valuable tool for a more realistic assessment of SRB abundance in the natural environment. The distribution of SRB was investigated in a coastal marine sediment by hybridization of membrane-immobilized rRNA with oligonucleotide probes. As represented by general probe–target groups, SRB rRNA contributed between 18% and 25% to the prokaryotic rRNA pool. The dominant SRB were related to complete oxidizing genera (Desulphococcus , Desulphosarcina and Desulphobacterium ), while Desulphobacter could not be detected. The vertical profile and quantity of rRNA from SRB was compared with sulphate reduction rates (SRR) measured with
35 SO4 2- tracer in whole-core incubations. While SRB abundance was highest near the surface, peaking at around 1.5 cm, measured sulphate reduction rates were lowest in this region. A second peak of SRB rRNA was observed at the transition zone from oxidized to reduced sediment, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI-stained cells indicated a population size for SRB of 2.4–6.1 × 108 cells cm-3 wet sediment. Cellular sulphate reduction rates calculated on the basis of these estimated cell numbers were between 0.01 and 0.09 fmol SO4 2- cell-1 day-1 , which is below the rates that have been determined for pure cultures (0.2–50 fmol SO4 2- cell-1 day-1 ) growing exponentially at near- optimal temperature with a surplus of substrates. [ABSTRACT FROM AUTHOR]- Published
- 1999
- Full Text
- View/download PDF
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