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Candry P, Abrahamson B, Stahl DA, Winkler MKH. Microbially mediated climate feedbacks from wetland ecosystems. Glob Chang Biol 2023; 29:5169-5183. [PMID: 37386740 DOI: 10.1111/gcb.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
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.
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Affiliation(s)
- Pieter Candry
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Britt Abrahamson
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - David Allan Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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Gorman-Lewis D, Martens-Habbena W, Stahl DA. Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea. Geobiology 2014; 12:157-171. [PMID: 24589203 DOI: 10.1111/gbi.12075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
The ammonia-oxidizing archaeon Nitrosopumilus maritimus strain SCM1 (strain SCM1), a representative of the Thaumarchaeota archaeal phylum, can sustain high specific rates of ammonia oxidation at ammonia concentrations too low to sustain metabolism by ammonia-oxidizing bacteria (AOB). One structural and biochemical difference between N. maritimus and AOB that might be related to the oligotrophic adaptation of strain SCM1 is the cell surface. A proteinaceous surface layer (S-layer) comprises the outermost boundary of the strain SCM1 cell envelope, as opposed to the lipopolysaccharide coat of Gram-negative AOB. In this work, we compared the surface reactivities of two archaea having an S-layer (strain SCM1 and Sulfolobus acidocaldarius) with those of four representative AOB (Nitrosospira briensis, Nitrosomonas europaea, Nitrosolobus multiformis, and Nitrosococcus oceani) using potentiometric and calorimetric titrations to evaluate differences in proton-ionizable surface sites. Strain SCM1 and S. acidocaldarius have a wider range of proton buffering (approximately pH 10-3.5) than the AOB (approximately pH 10-4), under the conditions investigated. Thermodynamic parameters describing proton-ionizable sites (acidity constants, enthalpies, and entropies of protonation) are consistent with these archaea having proton-ionizable amino acid side chains containing carboxyl, imidazole, thiol, hydroxyl, and amine functional groups. Phosphorous-bearing acidic functional groups, which might also be present, could be masked by imidazole and thiol functional groups. Parameters for the AOB are consistent with surface structures containing anionic oxygen ligands (carboxyl- and phosphorous-bearing acidic functional groups), thiols, and amines. In addition, our results showed that strain SCM1 has more reactive surface sites than the AOB and a high concentration of sites consistent with aspartic and/or glutamic acid. Because these alternative boundary layers mediate interaction with the local external environment, these data provide the basis for further comparisons of the thermodynamic behavior of surface reactivity toward essential nutrients.
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Affiliation(s)
- D Gorman-Lewis
- University of Washington, Department of Earth and Space Sciences, Seattle, WA, USA
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3
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Abstract
Ribosomal RNA (rRNA) sequences were used to establish the phylogenetic affiliations of symbioses in which prokaryotes appear to confer sulfur-based chemoautotrophy on their invertebrate hosts. Two submarine hydrothermal vent animals, the vestimentiferan tube worm Riftia pachyptila and the clam Calyptogena magnifica, and a tidal-flat bivalve, Solemya velum, were inspected. 5S rRNA's were extracted from symbiont-bearing tissues, separated into unique forms, and their nucleotide sequences determined and related to other 5S rRNA's in a phylogenetic tree analysis. The prokaryotic symbionts are related to one another and affiliated with the same narrow phylogenetic grouping as Escherichia coli and Pseudomonas aeruginosa. The sequence comparisons suggest that Riftia is more closely related to the bivalves than their current taxonomic status would suggest.
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Raskin L, Capman WC, Kane MD, Rittmann BE, Stahl DA. Critical evaluation of membrane supports for use in quantitative hybridizations. Appl Environ Microbiol 2010; 62:300-3. [PMID: 16535220 PMCID: PMC1388761 DOI: 10.1128/aem.62.1.300-303.1996] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The quantification of 16S rRNA by oligonucleotide probe hybridization was investigated with MagnaGraph (Micron Separation, Inc. [MSI]), Magna Charge (MSI), Magna (MSI), Immobilon-N (Millipore Corporation), and Nytran (Schleicher & Schuell, Inc.) membranes as supports for nucleic acid immobilization. The levels of detectability provided by the Magna Charge and Immobilon-N membranes were 20 to 50 times better than those obtained with the MagnaGraph, Magna, and Nytran membranes. The variability of the signal response for individual membranes ranged from 10 to 50%, with the Magna Charge and Immobilon-N membranes demonstrating the lowest variability.
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Raskin L, Rittmann BE, Stahl DA. Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl Environ Microbiol 2010; 62:3847-57. [PMID: 16535428 PMCID: PMC1388966 DOI: 10.1128/aem.62.10.3847-3857.1996] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The microbial population structure and function of natural anaerobic communities maintained in laboratory fixed-bed biofilm reactors were tracked before and after a major perturbation, which involved the addition of sulfate to the influent of a reactor that had previously been fed only glucose (methanogenic), while sulfate was withheld from a reactor that had been fed both glucose and sulfate (sulfidogenic). The population structure, determined by using phylogenetically based oligonucleotide probes for methanogens and sulfate-reducing bacteria, was linked to the functional performance of the biofilm reactors. Before the perturbation, the methanogenic reactor contained up to 25% methanogens as well as 15% sulfate-reducing bacteria, even though sulfate was not present in the influent of this reactor. Methanobacteriales and Desulfovibrio spp. were the most abundant methanogens and sulfate-reducing bacteria, respectively. The presence of sulfate-reducing bacteria (primarily Desulfovibrio spp. and Desulfobacterium spp.) in the absence of sulfate may be explained by their ability to function as proton-reducing acetogens and/or fermenters. Sulfate reduction began immediately following the addition of sulfate consistent with the presence of significant levels of sulfate-reducing bacteria in the methanogenic reactor, and levels of sulfate-reducing bacteria increased to a new steady-state level of 30 to 40%; coincidentally, effluent acetate concentrations decreased. Notably, some sulfate-reducing bacteria (Desulfococcus/Desulfosarcina/Desulfobotulus group) were more competitive without sulfate. Methane production decreased immediately following the addition of sulfate; this was later followed by a decrease in the relative concentration of methanogens, which reached a new steady-state level of approximately 8%. The changeover to sulfate-free medium in the sulfidogenic reactor did not cause a rapid shift to methanogenesis. Methane production and a substantial increase in the levels of methanogens were observed only after approximately 50 days following the perturbation.
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Smoot LM, Smoot JC, Smidt H, Noble PA, Könneke M, McMurry ZA, Stahl DA. DNA microarrays as salivary diagnostic tools for characterizing the oral cavity's microbial community. Adv Dent Res 2005; 18:6-11. [PMID: 15998937 DOI: 10.1177/154407370501800103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- L M Smoot
- Civil and Environmental Engineering, 302 More Hall, Box 352700, University of Washington, Seattle, WA 98195-2700, USA
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Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA. Persistence and functional impact of a microbial inoculant on native microbial community structure, nutrient digestion and fermentation characteristics in a rumen model. Syst Appl Microbiol 2002; 25:416-22. [PMID: 12421079 DOI: 10.1078/0723-2020-00125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Small sub-unit (SSU) rRNA-targeted oligonucleotide probes were used to monitor the persistence of a genetically engineered bacterium inoculated in model rumens. Eight dual flow continuous culture fermenters were operated with either standard artificial saliva buffer or buffer with chondroitin sulfate (0.5 g/l) added. After 168 h of operation, fermenters were inoculated with Bacteroides thetaiotaomicron BTX (BTX), at approximately 1% of total bacteria. B. thetaiotaomicron was quantified using a species-specific probe and shown to persist in fermenters 144 h after inoculation (relative abundance 0.48% and 1.42% of total SSU rRNA with standard and chondroitin sulfate buffers, respectively). No B. thetaiotaomicron SSU rRNA was detected in fermenter samples prior to inoculation with strain BTX. Relative abundances of Bacteria, Eucarya and Archaea were not affected by either inoculation or buffer type. Fiber digestion, in particular the hemicellulose fraction, increased after strain BTX addition. Chondroitin sulfate addition to the buffer increased bacterial nitrogen flow in fermenters, but did not alter fiber digestion. Neither inoculum nor buffer type altered total short chain fatty acid (VFA) concentrations but proportions of individual VFA differed. In model rumens, B. thetaiotaomicron BTX increased fiber digestion when added to mixed ruminal microbes, independent of chondroitin sulfate addition; but further study is needed to determine effects on other fiber-digesting bacteria.
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Affiliation(s)
- C J Ziemer
- Department of Animal Science, University of Minnesota, USA
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Becker JG, Berardesco G, Rittmann BE, Stahl DA. Successional changes in an evolving anaerobic chlorophenol-degrading community used to infer relationships between population structure and system-level processes. Appl Environ Microbiol 2001; 67:5705-14. [PMID: 11722926 PMCID: PMC93363 DOI: 10.1128/aem.67.12.5705-5714.2001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The response of a complex methanogenic sediment community to 2-chlorophenol (2-CP) was evaluated by monitoring the concentrations of this model contaminant and important metabolic intermediates and products and by using rRNA-targeted probes to track several microbial populations. Key relationships between the evolving population structure, formation of metabolic intermediates, and contaminant mineralization were identified. The nature of these relationships was intrinsically linked to the metabolism of benzoate, an intermediate that transiently accumulated during the mineralization of 2-CP. Before the onset of benzoate fermentation, reductive dehalogenation of 2-CP competed with methanogenesis for endogenous reducing equivalents. This suppressed H(2) levels, methane production, and archaeal small-subunit (SSU)-rRNA concentrations in the sediment community. The concentrations of bacterial SSU rRNA, including SSU rRNA derived from "Desulfovibrionaceae" populations, tracked with 2-CP levels, presumably reflecting changes in the activity of dehalogenating organisms. After the onset of benzoate fermentation, the abundance of Syntrophus-like SSU rRNA increased, presumably because these syntrophic organisms fermented benzoate to methanogenic substrates. Consequently, although the parent substrate 2-CP served as an electron acceptor, cleavage of its aromatic nucleus also influenced the sediment community by releasing the electron donors H(2) and acetate. Increased methane production and archaeal SSU-rRNA levels, which tracked with the Syntrophus-like SSU-rRNA concentrations, revealed that methanogenic populations in particular benefited from the input of reducing equivalents derived from 2-CP.
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Affiliation(s)
- J G Becker
- Department of Civil Engineering, Northwestern University, Evanston, IL 60208, USA.
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Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 2001; 183:6028-35. [PMID: 11567003 PMCID: PMC99682 DOI: 10.1128/jb.183.20.6028-6035.2001] [Citation(s) in RCA: 275] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genus Thermodesulfobacterium (a separate bacterial division) were monophyletic with delta-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that dsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the delta-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for a dsrAB lateral gene transfer event also was found within the delta-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes in Archaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.
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Affiliation(s)
- M Klein
- Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany
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10
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Abstract
The 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 (> 2.4x) 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.
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Affiliation(s)
- W T Liu
- Environmental Health Engineering Program, Department of Civil Engineering, Northwestern University, Evanston, IL 60208, USA.
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MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA. Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ Microbiol 2001; 67:3908-22. [PMID: 11525985 PMCID: PMC93109 DOI: 10.1128/aem.67.9.3908-3922.2001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2001] [Accepted: 06/21/2001] [Indexed: 11/20/2022] Open
Abstract
We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling site is at a depth of 100 m, with temperatures of 2 to 4 degrees C year-round. RNA extracted from sediment was probed with radiolabeled oligonucleotides targeting bacterial, archaeal, and eukaryotic SSU rRNAs, as well as with a universal probe. The coverage of these probes in relation to the present sequence database is discussed. Because ribosome production is growth rate regulated, rRNA concentrations are an indicator of the microbial populations active in situ. Over a 1-year period, changes in sedimentary SSU rRNA concentrations followed seasonal changes in surface water temperature and SSU rRNA concentration. Sedimentary depth profiles of oxygen, reduced manganese and iron, and sulfate changed relatively little from season to season, but the nitrate concentration was approximately fivefold higher in April and June 1997 than at the other times sampling was done. We propose that sediment microbial SSU rRNA concentrations at our sampling site are influenced by seasonal inputs from the water column, particularly the settling of the spring diatom bloom, and that the timing of this input may be modulated by grazers, such that ammonia becomes available to sediment microbes sooner than fresh organic carbon. Nitrate production from ammonia by autotrophic nitrifying bacteria, combined with low activity of heterotrophic denitrifying bacteria in the absence of readily degradable organic carbon, could account for the cooccurrence of high nitrate and low SSU rRNA concentrations.
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Affiliation(s)
- B J MacGregor
- Civil Engineering Department, Northwestern University, Evanston, Illinois 60208, USA.
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MacGregor BJ, Toze S, Alm EW, Sharp R, Ziemer CJ, Stahl DA. Distribution and abundance of Gram-positive bacteria in the environment: development of a group-specific probe. J Microbiol Methods 2001; 44:193-203. [PMID: 11240041 DOI: 10.1016/s0167-7012(00)00243-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We developed a 16S rRNA-targeted oligonucleotide probe (S-P-GPos-1200-a-A-13) for the Gram-positive bacteria, confirmed its specificity by database searches and hybridization studies, and investigated the effects of humic acids on membrane hybridizations with this probe. S-P-GPos-1200-a-A-13 was used to estimate the abundance of Gram-positive populations in the bovine rumen and Lake Michigan sediments. This probe should be useful for studies of the environmental distribution of Gram-positive bacteria and the detection of uncultured, phylogenetically Gram-positive bacteria with variable or negative Gram staining reactions, and could serve for Gram staining in some diagnostic settings.
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Affiliation(s)
- B J MacGregor
- Civil Engineering Department, Northwestern University, Evanston, IL 60208, USA
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MacGregor BJ, Van Mooy B, Baker BJ, Mellon M, Moisander PH, Paerl HW, Zehr J, Hollander D, Stahl DA. Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Environ Microbiol 2001; 3:205-19. [PMID: 11321537 DOI: 10.1046/j.1462-2920.2001.00180.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have used a combination of microbiological, molecular biological and stable isotope methods to relate specific microbial populations to elemental cycling at an offshore site in Lake Michigan. Several lines of evidence suggest that atmospheric N2 may be a significant source of nitrogen to the lake. Particulate organic nitrogen (PON) at approximately equals 10-15m depth in July and October had a delta15N of 0.5-1.5%o. These values closely reflect the 15N composition of atmospheric N2, suggesting biological nitrogen fixation. Historical data show a developing late-summer N:P minimum at approximately equals 15 m; low abundance of inorganic nitrogen relative to phosphorus favours species able to acquire atmospheric nitrogen. Microscopic examination of October water samples revealed abundant heterocystous cyanobacteria, including Nodularia sp. Potentially nitrogen-fixing Anabaena spp. have been found in Lake Michigan before but, to our knowledge, this is the first report of Nodularia. Finally, we have amplified both cyanobacterial and non-cyanobacterial nifH sequences (encoding the nitrogenase iron protein) from lakewater samples, evidence for the presence of bacteria capable of nitrogen fixation. The surface waters of Lake Michigan are considered to be phosphate limited in the stratified season and, under these conditions, energetically expensive nitrogen fixation is expected to be uncompetitive with assimilation of combined nitrogen. Our results suggest that, from both microbiological and biogeochemical perspectives, this may be an oversimplification.
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Affiliation(s)
- B J MacGregor
- Department of Civil Engineering, Northwestern University, Evanston, IL 60208, USA.
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Webb SM, Gaillard JF, Jackson BE, Stahl DA. An EXAFS study of zinc coordination in microbial cells. J Synchrotron Radiat 2001; 8:943-945. [PMID: 11512987 DOI: 10.1107/s0909049500020975] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2000] [Accepted: 12/21/2000] [Indexed: 05/23/2023]
Abstract
Five microbes were isolated from metal amended enrichment cultures derived from the sediments of a lake contaminated by a zinc smelter. Each of these organisms was grown in pure culture in the presence of zinc. Quick Extended X-ray Absorption Fine Structure (QEXAFS) spectroscopy was used to investigate the average coordination environment of the zinc associated with the microbial biomass. Fitting of the first coordination shell of zinc shows that significant differences exist for each microbial species examined. The coordination environment of zinc varies between sulfurs to six-fold nitrogen/oxygen. with two microbial strains showing mixed coordination shells. Further study is required in order to characterize these sites and their locations within the cell.
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Affiliation(s)
- S M Webb
- Department of Civil Engineering, Northwestern University, Evanston, IL 60208-3109, USA
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Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA. Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes. Environ Microbiol 2000; 2:632-43. [PMID: 11214796 DOI: 10.1046/j.1462-2920.2000.00146.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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 system may serve as a suitable tool for studying aspects of ruminal microbial ecology and may resolve some of the relationships between microbial community structure and function by providing control of experimental conditions.
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Affiliation(s)
- C J Ziemer
- Department of Animal Science, University of Minnesota, St Paul 55108, USA.
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Abstract
The sweeping and challenging changes in the health care industry emanating from the Balanced Budget Act of 1997 have exceeded those experienced by health care providers and consumers under the Tax Equity and Fiscal Responsibility Act of 1982, the Diagnosis Related Groupings in 1984, and the Resource-Based Relative Value Scale in 1992. To understand and cope with these changes, the financial impact of the Balanced Budget Act is examined in depth, particularly in terms of reimbursement or funding for all health care settings, providers, and medical education. The dramatic changes in the health care delivery process that have caused havoc and turmoil also are examined. For survival and growth under the Balanced Budget Act, reengineering strategies are presented. The ethical and social responsibilities that underlie the current and future impact of the Balanced Budget Act are analyzed to foster the principles of justice, fairness, and best interests of the public.
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Affiliation(s)
- D A Stahl
- D. A. Stahl & Associates, Northbrook, Illinois60062, USA
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Alm EW, Stahl DA. Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J Microbiol Methods 2000; 40:153-62. [PMID: 10699671 DOI: 10.1016/s0167-7012(00)00120-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A protocol was developed for the efficient recovery of intact, high molecular weight rRNA from different environmental matrices. Critical variables were identified in sample processing that influenced yield and integrity of recovered nucleic acid. Most notably, the order of addition and the buffer to sample volume ratio profoundly influenced the efficiency of nucleic acid recovery from sediment material when utilizing a guanidine thiocyanate-beta-mercaptoethaol extraction buffer. Addition of one sample volume to five buffer volumes contributed to an order of magnitude increase in recovery relative to reverse order of addition (buffer addition to sample). An optimized extraction protocol was used to evaluate rRNA yield by seeding samples with whole cells and radiolabeled nucleic acid. Recovery of intact rRNA was confirmed by polyacrylamide gel electrophoresis, which was also used to provide another estimate of quantity. This optimized protocol was used to measure depth-related changes in biomass distribution in Lake Michigan deep-water sediments. This revealed a biomodal biomass distribution; a maximum near the water/sediment interface and a secondary peak associated with the oxic/suboxic boundary. A significant portion of the community at the oxic/suboxic boundary was composed of non-methanogenic Archaea.
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Affiliation(s)
- E W Alm
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
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Caldwell DE, Colwell RR, Harayama S, Kjelleberg S, Givskov M, Molin S, Nielsen AT, Heydorn A, Tolker-Nielsen T, Sternberg C, Nealson K, Pace NR, Rainey P, Stackebrandt E, Tindall BJ, Stahl DA. Crystal ball: leading scientists in the field of environmental microbiology consider the technical and conceptual developments that they believe will drive innovative research during the first years of the new millennium. Environ Microbiol 2000; 2:3-10. [PMID: 11243260 DOI: 10.1046/j.1462-2920.2000.00099.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Benefield LE, Clifford J, Cox S, Hagenow NR, Hastings C, Kobs AE, Mayer GG, Porter-O'Grady T, Stahl DA, Valentine NM, Wolgin F. Nursing leaders predict top trends for 2000. Nurs Manag (Harrow) 2000; 31:21-3. [PMID: 10818935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Nursing Management's Editorial Advisory Board predicts the top 10 trends that will impact nurse leaders in 2000. Use them to lead in the new millennium.
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Affiliation(s)
- L E Benefield
- Harris College of Nursing, Texas Christian University, Ft. Worth, USA
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20
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Stahl DA. Poised for next-century politics? Nurs Manag (Harrow) 1999; 30:25-7. [PMID: 10818922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
From management hierarchies, to leveraging "who you know," to shared governance, organizational politics have changed over the years. Best bets for the future: Be a good leader, don't get hung up on titles, and value your employees.
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Affiliation(s)
- D A Stahl
- Stahl & Associates, Northbrook, Ill., USA
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21
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Becker JG, Stahl DA, Rittmann BE. Reductive dehalogenation and conversion of 2-chlorophenol to 3-chlorobenzoate in a methanogenic sediment community: implications for predicting the environmental fate of chlorinated pollutants. Appl Environ Microbiol 1999; 65:5169-72. [PMID: 10543840 PMCID: PMC91698 DOI: 10.1128/aem.65.11.5169-5172.1999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotransformation of 2-chlorophenol by a methanogenic sediment community resulted in the transient accumulation of phenol and benzoate. 3-Chlorobenzoate was a more persistent product of 2-chlorophenol metabolism. The anaerobic biotransformation of phenol to benzoate presumably occurred via para-carboxylation and dehydroxylation reactions, which may also explain the observed conversion of 2-chlorophenol to 3-chlorobenzoate.
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Affiliation(s)
- J G Becker
- Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208, USA.
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22
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Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 1999; 65:4375-84. [PMID: 10508063 PMCID: PMC91581 DOI: 10.1128/aem.65.10.4375-4384.1999] [Citation(s) in RCA: 371] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic lineages has been reported in coastal marine benthic environments. We investigated the relative abundance, vertical distribution, phylogenetic composition, and spatial variability of Archaea in deep-sea sediments collected from several stations in the Atlantic Ocean. Quantitative oligonucleotide hybridization experiments indicated that the relative abundance of archaeal 16S rRNA in deep-sea sediments (1500 m deep) ranged from about 2.5 to 8% of the total prokaryotic rRNA. Clone libraries of PCR-amplified archaeal rRNA genes (rDNA) were constructed from 10 depth intervals obtained from sediment cores collected at depths of 1,500, 2,600, and 4,500 m. Phylogenetic analysis of rDNA sequences revealed the presence of a complex archaeal population structure, whose members could be grouped into discrete phylogenetic lineages within the two kingdoms, Crenarchaeota and Euryarchaeota. Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population.
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Affiliation(s)
- C Vetriani
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901-8521, USA.
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23
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Minz D, Flax JL, Green SJ, Muyzer G, Cohen Y, Wagner M, Rittmann BE, Stahl DA. Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl Environ Microbiol 1999; 65:4666-71. [PMID: 10508104 PMCID: PMC91622 DOI: 10.1128/aem.65.10.4666-4671.1999] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline microbial mat and to evaluate their distribution in relation to levels of oxygen. The most highly diverse DSR sequences, most related to those of the Desulfonema-like organisms within the delta-proteobacteria, were recovered from oxic regions of the mat. This observation extends those of previous studies by us and others associating Desulfonema-like organisms with oxic habitats.
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Affiliation(s)
- D Minz
- Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208-3109, USA
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24
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Minz D, Fishbain S, Green SJ, Muyzer G, Cohen Y, Rittmann BE, Stahl DA. Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia. Appl Environ Microbiol 1999; 65:4659-65. [PMID: 10508103 PMCID: PMC91621 DOI: 10.1128/aem.65.10.4659-4665.1999] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-microm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families "Desulfovibrionaceae" and "Desulfobacteriaceae," Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.
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Affiliation(s)
- D Minz
- Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208-3109, USA
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25
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Nielsen AT, Liu WT, Filipe C, Grady L, Molin S, Stahl DA. Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor. Appl Environ Microbiol 1999; 65:1251-8. [PMID: 10049891 PMCID: PMC91172 DOI: 10.1128/aem.65.3.1251-1258.1999] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. The reactor was fed with media containing acetate and high levels of phosphate (P/C weight ratio, 8:100) but failed to completely remove phosphate in the effluent and showed very limited biological phosphorus removal activity. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA was used to investigate the bacterial diversity. Up to 11 DGGE bands representing at least 11 different sequence types were observed; DNA from the 6 most dominant of these bands was further isolated and sequenced. Comparative phylogenetic analysis of the partial 16S rRNA sequences suggested that one sequence type was affiliated with the alpha subclass of the Proteobacteria, one was associated with the Legionella group of the gamma subclass of the Proteobacteria, and the remaining four formed a novel group of the gamma subclass of the Proteobacteria with no close relationship to any previously described species. The novel group represented approximately 75% of the PCR-amplified DNA, based on the DGGE band intensities. Two oligonucleotide rRNA probes for this novel group were designed and used in a whole-cell hybridization analysis to investigate the abundance of this novel group in situ. The bacteria were coccoid and 3 to 4 microm in diameter and represented approximately 35% of the total population, suggesting a relatively close agreement with the results obtained by the PCR-based DGGE method. Further, based on electron microscopy and standard staining microscopic analysis, this novel group was able to accumulate granule inclusions, possibly consisting of polyhydroxyalkanoate, inside the cells.
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Affiliation(s)
- A T Nielsen
- Department of Microbiology, Technical University of Denmark, Lyngby, Denmark
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26
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Sahm K, MacGregor BJ, Jørgensen BB, Stahl DA. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1999; 1:65-74. [PMID: 11207719 DOI: 10.1046/j.1462-2920.1999.00007.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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 35SO4(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 x 10(8) 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 nearoptimal temperature with a surplus of substrates.
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Affiliation(s)
- K Sahm
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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27
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Abstract
To prepare for the Transfer Rule's financial impact, nurse leaders should understand these issues, ramifications, and strategies.
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Affiliation(s)
- D A Stahl
- D.A. Stahl and Associates, Northbrook, Ill., USA
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28
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McMahon KD, Stahl DA, Raskin L. A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment. Microb Ecol 1998; 36:362-371. [PMID: 9852515 DOI: 10.1007/s002489900122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Abstract Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro-transcribed and native rRNA indicated that, when in vitro-transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro-transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.
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Affiliation(s)
- KD McMahon
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA
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29
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Stahl DA. Strategic planning for postacute care. Nurs Manag (Harrow) 1998; 29:6-9. [PMID: 9987338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The author examines workable approaches and benefits of using strategic planning to prepare for future postacute care.
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30
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Noguera DR, Brusseau GA, Rittmann BE, Stahl DA. A unified model describing the role of hydrogen in the growth of desulfovibrio vulgaris under different environmental conditions. Biotechnol Bioeng 1998; 59:732-46. [PMID: 10099394 DOI: 10.1002/(sici)1097-0290(19980920)59:6<732::aid-bit10>3.0.co;2-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A unified model for the growth of Desulfovibrio vulgaris under different environmental conditions is presented. The model assumes the existence of two electron transport mechanisms functioning simultaneously. One mechanism results in the evolution and consumption of hydrogen, as in the hydrogen-cycling model. The second mechanism assumes a direct transport of electrons from the donor to the acceptor, without the participation of H2. A combination of kinetic and thermodynamic conditions control the flow of electrons through each pathway. The model was calibrated using batch experiments with D. vulgaris grown on lactate, in the presence and absence of sulfate, and was verified using additional batch experiments under different conditions. The model captured the general trends of consumption of substrates and accumulation of products, including the transient accumulation and consumption of H2. Furthermore, the model estimated that 48% of the electrons transported from lactate to sulfate involved H2 production, indicating that hydrogen cycling is a fundamental process in D. vulgaris. The presence of simultaneous electron transport mechanisms might provide D. vulgaris with important ecological advantages, because it facilitates a rapid response to changes in environmental conditions. This model increases our ability to study the microbial ecology of anaerobic environments and the role of Desulfovibrio species in a variety of environments. Copyright 1998 John Wiley & Sons, Inc.
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Affiliation(s)
- DR Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706-1691, USA
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31
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Stahl DA. The risks and rewards of contracting with health plans. Nurs Manag (Harrow) 1998; 29:18-21. [PMID: 9807467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Contracting with health plans isn't only the right strategy under PPS; it's the mechanism that will reposition the postacute care provider for success in the health care arena of the 21st century.
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32
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Stahl DA. PPS challenges in postacute care. Nurs Manag (Harrow) 1998; 29:10-2. [PMID: 9807382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The challenges the prospective payment system (PPS) pose to managers in postacute care are enormous. Managers need to learn not only how to prepare their facilities and staff for PPS but also, and more important, how to provide the leadership to carry out a strategic plan for survival. In effect, this new reimbursement system, based on 44 resource utilization groups (RUGS III)--each with a distinct payment level--will necessitate a reexamination of managerial competencies.
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Affiliation(s)
- D A Stahl
- D.A. Stahl and Associates, Northbrook, Ill., USA
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33
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Stahl DA. The nuts and bolts of prospective payment. Nurs Manag (Harrow) 1998; 29:20-3. [PMID: 9807444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
How does a skilled nursing facility survive and thrive under the prospective payment system (PPS)? To begin, PPS risks must be fully understood and managed in terms of the Resource Utilization Groups Version III (RUGS III) and the Minimum Data Set (MDS) 2.0. Second, strategies for change within the organization must be developed and implemented. Third, managing costs under the PPS must become the priority.
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34
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Wagner M, Roger AJ, Flax JL, Brusseau GA, Stahl DA. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 1998; 180:2975-82. [PMID: 9603890 PMCID: PMC107267 DOI: 10.1128/jb.180.11.2975-2982.1998] [Citation(s) in RCA: 537] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/1998] [Accepted: 03/24/1998] [Indexed: 02/07/2023] Open
Abstract
Microorganisms that use sulfate as a terminal electron acceptor for anaerobic respiration play a central role in the global sulfur cycle. Here, we report the results of comparative sequence analysis of dissimilatory sulfite reductase (DSR) genes from closely and distantly related sulfate-reducing organisms to infer the evolutionary history of DSR. A 1.9-kb DNA region encoding most of the alpha and beta subunits of DSR could be recovered only from organisms capable of dissimilatory sulfate reduction with a PCR primer set targeting highly conserved regions in these genes. All DNA sequences obtained were highly similar to one another (49 to 89% identity), and their inferred evolutionary relationships were nearly identical to those inferred on the basis of 16S rRNA. We conclude that the high similarity of bacterial and archaeal DSRs reflects their common origin from a conserved DSR. This ancestral DSR was either present before the split between the domains Bacteria, Archaea, and Eucarya or laterally transferred between Bacteria and Archaea soon after domain divergence. Thus, if the physiological role of the DSR was constant over time, then early ancestors of Bacteria and Archaea already possessed a key enzyme of sulfate and sulfite respiration.
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Affiliation(s)
- M Wagner
- Department of Civil Engineering, Technological Institute, Northwestern University, Evanston, Illinois 60208-3109, USA
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35
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Stahl DA. Consolidated billing and compliance program--Part 2. Nurs Manag (Harrow) 1998; 29:12-5. [PMID: 9807420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
On February 11, 1998, the Department of Health and Human Services Office of Inspector General (OIG) released guidelines to assist hospitals and their agents and subproviders to comply with Medicare and Medicaid regulations. While adopting and implementing a compliance program is voluntary, the OIG believes that such a program prevents fraud, abuse, and waste while simultaneously furthering providers' fundamental mission--to provide quality care.
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36
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Stahl DA. Consolidated billing and compliance program--Part 1. Nurs Manag (Harrow) 1998; 29:16-8. [PMID: 9807404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The consolidated billing requirement of the Balanced Budget Act of 1997, which becomes effective on July 1, 1998, has catapulted postacute care providers into the arena of vulnerability for possible fraud and abuse. With this in mind, the postacute care providers must identify the implications and develop and implement a compliance program to prevent fraud, abuse and waste.
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37
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Stahl DA. Leadership in these changing times. Nurs Manag (Harrow) 1998; 29:16-8. [PMID: 9697487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The six ingredients for success in the leadership of a postacute care facility often are not exercised--much to the detriment of their organizations. Without strong leadership, people in the facility will not do what needs to be done to succeed under managed care, the BBA of 1997 and the PPS. In these changing and difficult times in health care, the challenge of leadership is to attain the vision of the organization, which, in turn, demands strong leadership.
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38
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Stahl DA. Subacute care: creating alternatives. Reengineering: the key to survival and growth under PPS. Nurs Manag (Harrow) 1998; 29:14-7. [PMID: 9544024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many postacute care providers are concerned about the effects of the prospective payment system on skilled nursing facilities. To retain their contractual arrangements, physical, occupational and speech therapists are trying to develop services within the financial constraints the PPS imposed. Management and staff of SNFs also are struggling with the Resource Utilization Groups III and the Minimum Data Set that will be the basis for the predetermined, per diem, all-inclusive fixed rate to be paid. The most logical approach to dealing with this crisis is to reengineer all of the SNFs' processes.
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39
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Stahl DA. Achieving a competitive advantage in managed care. Nurs Manag (Harrow) 1998; 29:18-21. [PMID: 9496092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
When building a competitive advantage to thrive in the managed care arena, subacute care providers are urged to be revolutionary rather than reactionary, proactive rather than passive, optimistic rather than pessimistic and growth-oriented rather than cost-reduction oriented. Weaknesses must be addressed aggressively. To achieve a competitive edge, assess the facility's strengths, understand the marketplace and comprehend key payment methods.
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40
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Stahl DA. Growth through capitation and physician practice management. Nurs Manag (Harrow) 1998; 29:14-6. [PMID: 9479150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Capitation achieves a competitive edge, yet many subacute care providers have not aggressively pursued this strategy. To take steps toward capitation, the following points need to be addressed: (1) determine what type of capitation to pursue; (2) establish the proper infrastructure to support capitated services; (3) implement a case management system; and (4) practice total quality management.
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41
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Stahl DA. Anatomy of a management system. Nurs Manag (Harrow) 1997; 28:20-1. [PMID: 9423446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
While a Management System is no panacea for success in managed care, not having such a system can be bazardous to the health of a subacute care facility. The eight components of the Management System and how they relate to subacute care are discussed.
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42
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Stahl DA. Balanced Budget Act of 1997: what it means for subacute care. Nurs Manag (Harrow) 1997; 28:28-9. [PMID: 9385152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Balanced Budget Act of 1997 calls for significant changes in the Medicaid and Medicare programs. Three measures help subacute care providers to meet the changes this act poses: (1) understanding a prospective payment system; (2) developing a financial model; and (3) implementing efficient systems that decrease cost.
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43
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Stahl DA. Managing risks in subacute care. Nurs Manag (Harrow) 1997; 28:26-7. [PMID: 9369717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Risk management should improve the quality of care and clinical outcomes as well as prevent litigation. A systematic risk-management program needs objectives, goals, benchmarks and a continuous quality improvement approach. Three basic tenets help: quality, evaluation and utilization management.
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44
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Abstract
An obligately methylotrophic organism was isolated from a water well that manifested symptoms of biofouling. The isolate was appendaged and utilized methylamine, dimethylamine, trimethylamine, or methanol as the sole carbon and energy source. The isolate exhibited hydroxypyruvate reductase activity, suggesting C1-assimilation via the serine pathway. Fatty acid profiling indicated the predominance of 18:1 cis-fatty acids. The isolate did not grow anaerobically with nitrate as the final electron acceptor. Genomic DNA from the isolate did not hybridize against the narG gene, which encodes the alpha subunit of dissimilatory nitrate reductase in Escherichia coli. The phenotypic data suggested the assignment of the isolate to the genus Hyphomicrobium. The identification was supported by phylogenetic characterization based on 16S rRNA sequence comparisons of the isolate.
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Affiliation(s)
- L Tuhela
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
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45
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Stahl DA. Managing fraud and abuse risks. Subacute care: creating alternatives. Nurs Manag (Harrow) 1997; 28:22-4. [PMID: 9335834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fraud and abuse risks in subacute care concern three major areas: (1) inadequate treatment and quality of care; (2) underutilization of services; and (3) misrepresentation of service capabilities. Strategies on how to manage these risks and guide changes are given.
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Stahl DA. Quality measures: meeting consumer needs. Nurs Manag (Harrow) 1997; 28:20-1. [PMID: 9325945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Researchers have found that health care consumers do not necessarily accept quality outcomes measurements. What consumers define as quality may not be in sync with what the experts consider quality. Health care providers need to focus on three areas of outcome measures (1) access to services, (2) communication/coordination and (3) values.
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Stahl DA. Health care networks: opportunities and threats for subacute care. Nurs Manag (Harrow) 1997; 28:28-9. [PMID: 9325930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To retool and prepare for the trends that facilitate growth, subacute care providers must understand the complexity of relationships among key players--provider sponsored networks, physician practice management and managed care organizations. Providers need to reengineer contracting, relationships and marketing.
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Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 1997; 63:2397-402. [PMID: 9172361 PMCID: PMC168533 DOI: 10.1128/aem.63.6.2397-2402.1997] [Citation(s) in RCA: 246] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The utility of parallel hybridization of environmental nucleic acids to many oligonucleotides immobilized in a matrix of polyacrylamide gel pads on a glass slide (oligonucleotide microchip) was evaluated. Oligonucleotides complementary to small-subunit rRNA sequences of selected microbial groups, encompassing key genera of nitrifying bacteria, were shown to selectively retain labeled target nucleic acid derived from either DNA or RNA forms of the target sequences. The utility of varying the probe concentration to normalize hybridization signals and the use of multicolor detection for simultaneous quantitation of multiple probe-target populations were demonstrated.
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Affiliation(s)
- D Y Guschin
- Joint Human Genome Program, Argonne National Laboratory, Illinois 60439, USA
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Stahl DA. Customer service: the key to market differentiation. Nurs Manag (Harrow) 1997; 28:25-8. [PMID: 9325906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fierce competition in the subacute care environment makes customer service orientation essential. Four steps help to achieve quality customer service are: (1) institute core values; (2) identify your customers; (3) understand human resources; and (4) establish an efficient system.
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Stahl DA. Direct contracting: a new wave for subacute care. Nurs Manag (Harrow) 1997; 28:22-3. [PMID: 9287788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Direct contracting, called "the wave of the future," poses particular challenges in two key areas for subacute care providers: quality of care and price. Using this process, employer groups bypass managed care organizations and directly contract with health care providers.
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