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1.
ISME J ; 13(11): 2817-2833, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31320727

RESUMO

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 µm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.


Assuntos
Ferro/metabolismo , Microbiota , Plâncton/genética , Plâncton/virologia , California , Cilióforos/genética , Cilióforos/metabolismo , Cilióforos/efeitos da radiação , Cilióforos/virologia , Diatomáceas/genética , Diatomáceas/metabolismo , Diatomáceas/efeitos da radiação , Diatomáceas/virologia , Dinoflagellida/genética , Dinoflagellida/metabolismo , Dinoflagellida/efeitos da radiação , Dinoflagellida/virologia , Cadeia Alimentar , Haptófitas/genética , Haptófitas/metabolismo , Haptófitas/efeitos da radiação , Haptófitas/virologia , Oceanos e Mares , Fotossíntese , Fitoplâncton/genética , Fitoplâncton/metabolismo , Fitoplâncton/efeitos da radiação , Fitoplâncton/virologia , Plâncton/metabolismo , Plâncton/efeitos da radiação , Transcrição Gênica , Fenômenos Fisiológicos Virais , Vírus/genética
2.
Appl Environ Microbiol ; 81(10): 3442-50, 2015 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-25769822

RESUMO

Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low-comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls-these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria. Escherichia coli cells were engineered to produce lycopene, ß-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing E. coli. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in E. coli and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.


Assuntos
Escherichia coli/química , Escherichia coli/metabolismo , Rodopsina/metabolismo , Cor , Eletroforese em Gel de Poliacrilamida , Escherichia coli/genética , Expressão Gênica , Microscopia de Fluorescência , Dados de Sequência Molecular , Rodopsina/química , Rodopsina/genética
3.
Geobiology ; 12(4): 322-39, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24923179

RESUMO

Ferruginous Lake Matano, Indonesia hosts one of the deepest anoxygenic photosynthetic communities on Earth. This community is dominated by low-light adapted, BChl e-synthesizing green sulfur bacteria (GSB), which comprise ~25% of the microbial community immediately below the oxic-anoxic boundary (OAB; 115-120 m in 2010). The size of this community is dependent on the mixing regime within the lake and the depth of the OAB-at ~117 m, the GSB live near their low-light limit. Slow growth and C-fixation rates suggest that the Lake Matano GSB can be supported by sulfide even though it only accumulates to scarcely detectable (low µm to nm) concentrations. A model laboratory strain (Chlorobaculum tepidum) is indeed able to access HS- for oxidation at nm concentrations. Furthermore, the GSB in Lake Matano possess a full complement of S-oxidizing genes. Together, this physiological and genetic information suggests that deep-water GSB can be supported by a S-cycle, even under ferruginous conditions. The constraints we place on the metabolic capacity and physiology of GSB have important geobiological implications. Biomarkers diagnostic of GSB would be a good proxy for anoxic conditions but could not discriminate between euxinic and ferruginous states, and though GSB biomarkers could indicate a substantial GSB community, such a community may exist with very little metabolic activity. The light requirements of GSB indicate that at light levels comparable to those in the OAB of Lake Matano or the Black Sea, GSB would have contributed little to global ocean primary production, nutrient cycling, and banded iron formation (BIF) deposition in the Precambrian. Before the proliferation of oxygenic photosynthesis, shallower OABs and lower light absorption in the ocean's surface waters would have permitted greater light availability to GSB, potentially leading to a greater role for GSB in global biogeochemical cycles.


Assuntos
Chlorobi/metabolismo , Ferro/metabolismo , Lagos/química , Fotossíntese , Anaerobiose , Ferro/análise , Luz , Consórcios Microbianos , Pigmentos Biológicos/análise
4.
ISME J ; 7(8): 1556-67, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23619306

RESUMO

Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host-symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry.


Assuntos
Metabolismo Energético , Fontes Hidrotermais , Nitrogênio/metabolismo , Proteobactérias/fisiologia , Caramujos/microbiologia , Simbiose , Transcriptoma , Animais , Crescimento Quimioautotrófico , Elementos de DNA Transponíveis/genética , Flagelos/genética , Hidrogênio/metabolismo , Filogenia , Proteobactérias/genética , Proteobactérias/metabolismo
5.
Proc Natl Acad Sci U S A ; 104(13): 5590-5, 2007 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-17372221

RESUMO

Proteorhodopsins (PRs) are retinal-containing proteins that catalyze light-activated proton efflux across the cell membrane. These photoproteins are known to be globally distributed in the ocean's photic zone, and they are found in a diverse array of Bacteria and Archaea. Recently, light-enhanced growth rates and yields have been reported in at least one PR-containing marine bacterium, but the physiological basis of light-activated growth stimulation has not yet been determined. To describe more fully PR photosystem genetics and biochemistry, we functionally surveyed a marine picoplankton large-insert genomic library for recombinant clones expressing PR photosystems in vivo. Our screening approach exploited transient increases in vector copy number that significantly enhanced the sensitivity of phenotypic detection. Two genetically distinct recombinants, initially identified by their orange pigmentation, expressed a small cluster of genes encoding a complete PR-based photosystem. Genetic and biochemical analyses of transposon mutants verified the function of gene products in the photopigment and opsin biosynthetic pathways. Heterologous expression of six genes, five encoding photopigment biosynthetic proteins and one encoding a PR, generated a fully functional PR photosystem that enabled photophosphorylation in recombinant Escherichia coli cells exposed to light. Our results demonstrate that a single genetic event can result in the acquisition of phototrophic capabilities in an otherwise chemoorganotrophic microorganism, and they explain in part the ubiquity of PR photosystems among diverse microbial taxa.


Assuntos
Regulação da Expressão Gênica de Plantas , Rodopsina/genética , Trifosfato de Adenosina/química , Proteínas Arqueais/química , Proteínas de Bactérias/química , Membrana Celular/metabolismo , Escherichia coli/metabolismo , Biblioteca Gênica , Transferência Genética Horizontal , Luz , Modelos Químicos , Modelos Genéticos , Dados de Sequência Molecular , Fosforilação , Complexo de Proteínas do Centro de Reação Fotossintética , Rodopsinas Microbianas
6.
Microb Ecol ; 48(4): 473-88, 2004 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-15696381

RESUMO

Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.


Assuntos
Bactérias/classificação , Cromossomos Artificiais Bacterianos/genética , RNA Bacteriano/genética , RNA Ribossômico/genética , Microbiologia da Água , Bactérias/genética , California , DNA Intergênico , Biblioteca Gênica , Genes Bacterianos , Dados de Sequência Molecular , Oceano Pacífico , Filogenia
7.
Appl Environ Microbiol ; 68(1): 316-25, 2002 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-11772641

RESUMO

A coastal marine sulfide-oxidizing autotrophic bacterium produces hydrophilic filamentous sulfur as a novel metabolic end product. Phylogenetic analysis placed the organism in the genus Arcobacter in the epsilon subdivision of the Proteobacteria. This motile vibrioid organism can be considered difficult to grow, preferring to grow under microaerophilic conditions in flowing systems in which a sulfide-oxygen gradient has been established. Purified cell cultures were maintained by using this approach. Essentially all 4',6-diamidino-2-phenylindole dihydrochloride-stained cells in a flowing reactor system hybridized with Arcobacter-specific probes as well as with a probe specific for the sequence obtained from reactor-grown cells. The proposed provisional name for the coastal isolate is "Candidatus Arcobacter sulfidicus." For cells cultured in a flowing reactor system, the sulfide optimum was higher than and the CO(2) fixation activity was as high as or higher than those reported for other sulfur oxidizers, such as Thiomicrospira spp. Cells associated with filamentous sulfur material demonstrated nitrogen fixation capability. No ribulose 1,5-bisphosphate carboxylase/oxygenase could be detected on the basis of radioisotopic activity or by Western blotting techniques, suggesting an alternative pathway of CO(2) fixation. The process of microbial filamentous sulfur formation has been documented in a number of marine environments where both sulfide and oxygen are available. Filamentous sulfur formation by "Candidatus Arcobacter sulfidicus" or similar strains may be an ecologically important process, contributing significantly to primary production in such environments.


Assuntos
Arcobacter/classificação , Arcobacter/crescimento & desenvolvimento , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Sulfetos/metabolismo , Enxofre/metabolismo , Arcobacter/química , Arcobacter/genética , Arcobacter/metabolismo , Dióxido de Carbono/metabolismo , Meios de Cultura , DNA Ribossômico/análise , Hibridização in Situ Fluorescente , Microscopia Eletrônica , Dados de Sequência Molecular , Fixação de Nitrogênio , Oxirredução , Filogenia , Ribulose-Bifosfato Carboxilase/metabolismo , Análise de Sequência de DNA
8.
J Am Coll Cardiol ; 38(5): 1416-23, 2001 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-11691517

RESUMO

OBJECTIVES: The objective of this study was to identify preprocedure patient factors associated with percutaneous intervention costs and to examine the impact of these patient factors on economic profiles of interventional cardiologists. BACKGROUND: There is increasing demand for information about comparative resource use patterns of interventional cardiologists. Economic provider profiles, however, often fail to account for patient characteristics. METHODS: Data were obtained from Duke Medical Center cost and clinical information systems for 1,949 procedures performed by 13 providers between July 1, 1997, and December 31, 1998. Patient factors that influenced cost were identified using multiple regression analysis. After assessing interprovider variation in unadjusted cost, mixed linear models were used to examine how much cost variability was associated with the provider when patient characteristics were taken into account. RESULTS: Total hospital costs averaged $15,643 (median, $13,809), $6,515 of which represented catheterization laboratory costs. Disease severity, acuity, comorbid illness and lesion type influenced total costs (R(2) = 38%), whereas catheterization costs were affected by lesion type and acuity (R(2) = 32%). Patient characteristics varied significantly among providers. Unadjusted total costs were weakly associated with provider, and this association disappeared after accounting for patient factors. The provider influence on catheterization costs persisted after adjusting for patient characteristics. Furthermore, the pattern of variation changed: the adjusted analysis identified three new outliers, and two providers lost their outlier status. Only one provider was consistently identified as an outlier in the unadjusted and adjusted analyses. CONCLUSIONS: Economic profiles of interventional cardiologists may be misleading if they do not adequately adjust for patient characteristics before procedure.


Assuntos
Angioplastia Coronária com Balão/economia , Cateterismo Cardíaco/economia , Serviço Hospitalar de Cardiologia/economia , Doença das Coronárias/diagnóstico , Doença das Coronárias/economia , Interpretação Estatística de Dados , Custos Hospitalares/estatística & dados numéricos , Modelos Econométricos , Padrões de Prática Médica/economia , Risco Ajustado , Centros Médicos Acadêmicos , Idoso , Angioplastia Coronária com Balão/estatística & dados numéricos , Viés , Cateterismo Cardíaco/estatística & dados numéricos , Comorbidade , Doença das Coronárias/fisiopatologia , Grupos Diagnósticos Relacionados/classificação , Grupos Diagnósticos Relacionados/economia , Feminino , Pesquisa sobre Serviços de Saúde , Humanos , Tempo de Internação/economia , Modelos Lineares , Masculino , Pessoa de Meia-Idade , North Carolina , Padrões de Prática Médica/estatística & dados numéricos , Estudos Retrospectivos , Fatores de Risco , Índice de Gravidade de Doença , Volume Sistólico
9.
J Am Coll Cardiol ; 37(3): 885-92, 2001 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-11693766

RESUMO

OBJECTIVES: We sought to develop national benchmarks for valve replacement surgery by developing statistical risk models of operative mortality. BACKGROUND: National risk models for coronary artery bypass graft surgery (CABG) have gained widespread acceptance, but there are no similar models for valve replacement surgery. METHODS: The Society of Thoracic Surgeons National Cardiac Surgery Database was used to identify risk factors associated with valve surgery from 1994 through 1997. The population was drawn from 49,073 patients undergoing isolated aortic valve replacement (AVR) or mitral valve replacement (MVR) and from 43,463 patients undergoing CABG combined with AVR or MVR. Two multivariable risk models were developed: one for isolated AVR or MVR and one for CABG plus AVR or CABG plus MVR. RESULTS: Operative mortality rates for AVR, MVR, combined CABG/AVR and combined CABG/ MVR were 4.00%, 6.04%, 6.80% and 13.29%, respectively. The strongest independent risk factors were emergency/salvage procedures, recent infarction, reoperations and renal failure. The c-indexes were 0.77 and 0.74 for the isolated valve replacement and combined CABG/valve replacement models, respectively. These models retained their predictive accuracy when applied to a prospective patient population undergoing operation from 1998 to 1999. The Hosmer-Lemeshow goodness-of-fit statistic was 10.6 (p = 0.225) for the isolated valve replacement model and 12.2 (p = 0.141) for the CABG/valve replacement model. CONCLUSIONS: Statistical models have been developed to accurately predict operative mortality after valve replacement surgery. These models can be used to enhance quality by providing a national benchmark for valve replacement surgery.


Assuntos
Implante de Prótese de Valva Cardíaca/mortalidade , Idoso , Valva Aórtica/cirurgia , Ponte de Artéria Coronária/mortalidade , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Valva Mitral/cirurgia , Modelos Estatísticos , Medição de Risco , Fatores de Risco
10.
Stat Med ; 20(16): 2505-32, 2001 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-11512139

RESUMO

With the proliferation of clinical data registries and the rising expense of clinical trials, observational data sources are increasingly providing evidence for clinical decision making. These data are viewed as complementary to randomized clinical trials (RCT). While not as rigorous a methodological design, observational studies yield important information about effectiveness of treatment, as compared with the efficacy results of RCTs. In addition, these studies often have the advantage of providing longer-term follow-up, beyond that of clinical trials. Hence, they are useful for assessing and comparing patients' long-term prognosis under different treatment strategies. For patients with coronary artery disease, many observational comparisons have focused on medical therapy versus interventional procedures. In addition to the well-studied problem of treatment selection bias (which is not the focus of the present study), three significant methodological problems must be addressed in the analysis of these data: (i) designation of the therapeutic arms in the presence of early deaths, withdrawals, and treatment cross-overs; (ii) identification of an equitable starting point for attributing survival time; (iii) site to site variability in short-term mortality. This paper discusses these issues and suggests strategies to deal with them. A proposed methodology is developed, applied and evaluated on a large observational database that has long-term follow-up on nearly 10 000 patients.


Assuntos
Análise de Variância , Doença das Coronárias/mortalidade , Doença das Coronárias/terapia , Coleta de Dados , Interpretação Estatística de Dados , Previsões , Observação/métodos , Prognóstico , Modelos de Riscos Proporcionais , Sistema de Registros , Projetos de Pesquisa/normas , Estudos Cross-Over , Árvores de Decisões , Humanos , Pacientes Desistentes do Tratamento/estatística & dados numéricos , Seleção de Pacientes , Fatores de Risco , Viés de Seleção , Análise de Sobrevida , Fatores de Tempo , Resultado do Tratamento , Estados Unidos/epidemiologia
11.
Nature ; 411(6839): 786-9, 2001 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-11459054

RESUMO

Proteorhodopsin, a retinal-containing integral membrane protein that functions as a light-driven proton pump, was discovered in the genome of an uncultivated marine bacterium; however, the prevalence, expression and genetic variability of this protein in native marine microbial populations remain unknown. Here we report that photoactive proteorhodopsin is present in oceanic surface waters. We also provide evidence of an extensive family of globally distributed proteorhodopsin variants. The protein pigments comprising this rhodopsin family seem to be spectrally tuned to different habitats--absorbing light at different wavelengths in accordance with light available in the environment. Together, our data suggest that proteorhodopsin-based phototrophy is a globally significant oceanic microbial process.


Assuntos
Bactérias/química , Rodopsina/análise , Sequência de Aminoácidos , Animais , Membrana Celular/química , Clonagem Molecular , Escherichia coli , Biblioteca Gênica , Hibridização in Situ Fluorescente , Luz , Dados de Sequência Molecular , Oceanos e Mares , Plâncton/química , Reação em Cadeia da Polimerase , Retinaldeído/química , Rodopsina/classificação , Rodopsina/genética , Rodopsinas Microbianas , Água do Mar/análise , Microbiologia da Água
12.
Science ; 293(5529): 484-7, 2001 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-11463914

RESUMO

Microorganisms living in anoxic marine sediments consume more than 80% of the methane produced in the world's oceans. In addition to single-species aggregates, consortia of metabolically interdependent bacteria and archaea are found in methane-rich sediments. A combination of fluorescence in situ hybridization and secondary ion mass spectrometry shows that cells belonging to one specific archaeal group associated with the Methanosarcinales were all highly depleted in 13C (to values of -96 per thousand). This depletion indicates assimilation of isotopically light methane into specific archaeal cells. Additional microbial species apparently use other carbon sources, as indicated by significantly higher 13C/12C ratios in their cell carbon. Our results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms.


Assuntos
Deltaproteobacteria/metabolismo , Sedimentos Geológicos/microbiologia , Metano/metabolismo , Methanosarcinales/metabolismo , Anaerobiose , Isótopos de Carbono/análise , Deltaproteobacteria/química , Deltaproteobacteria/classificação , Hibridização in Situ Fluorescente , Lipídeos/análise , Methanosarcinales/química , Methanosarcinales/classificação , Oceanos e Mares , Sondas de Oligonucleotídeos , Oxirredução , Filogenia , RNA Arqueal/genética , RNA Bacteriano/genética , RNA Ribossômico/genética , Espectrometria de Massa de Íon Secundário , Sulfatos/metabolismo
13.
Environ Microbiol ; 3(5): 323-31, 2001 May.
Artigo em Inglês | MEDLINE | ID: mdl-11422319

RESUMO

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.


Assuntos
Bactérias/classificação , Bactérias/genética , DNA Ribossômico/genética , Óperon/genética , Filogenia , RNA Ribossômico/genética , Microbiologia da Água , Bactérias/citologia , Sequência de Bases , Clonagem Molecular , Biologia Marinha , Dados de Sequência Molecular , RNA de Transferência/genética
14.
Curr Opin Microbiol ; 4(3): 290-5, 2001 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-11378481

RESUMO

A remarkable array of new discoveries is emerging from studies of naturally occurring marine microbes. These discoveries originate from novel applications of evolving technologies, ranging from molecular phylogenetics to stable isotope analyses, to advanced microscopic techniques, to genomics. As a consequence, new perspectives on the natural history of marine microbes, the inseparable nature of the geological and biological worlds, and a plethora of unexpected new genotypes, phenotypes and physiologies are now being revealed. As our observations of naturally occurring microbes become increasingly more sophisticated, so will theory, technical applications and predictive capabilities in microbial ecology.


Assuntos
Biologia Marinha/tendências , Microbiologia da Água , Animais , Ecologia , Genômica , Humanos , Oceanos e Mares , Filogenia , Plâncton
15.
Circulation ; 103(17): 2133-7, 2001 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-11331252

RESUMO

BACKGROUND: The purpose of this study was to evaluate whether women undergoing cardiac surgery are more likely to suffer neurological complications than men and whether these complications could explain, at least in part, their higher perioperative mortality. METHODS AND RESULTS: The Society of Thoracic Surgery National Cardiac Surgery Database was examined for the years 1996 and 1997 to determine the frequency of new neurological events (stroke, transient ischemic attack, or coma) occurring after cardiac surgery. We reviewed clinical information on 416 347 patients (32% women) for whom complete neurological outcome data were available. New neurological events after surgery were higher for women than for men (3.8% versus 2.4%, P=0.001). For the whole group, the 30-day mortality was higher for women than for men (5.7% versus 3.5%, P=0.001), and among those patients who suffered a perioperative neurological event, mortality was also significantly higher for women than men (32% versus 28%, P=0.001). After adjustment for other risk factors (eg, age, history of hypertension and/or diabetes, duration of cardiopulmonary bypass, and other comorbid conditions) by multivariable logistic regression, female sex was independently associated with significantly higher risk of suffering new neurological events after cardiac surgery (OR 1.21, 95% CI 1.14 to 1.28, P=0.001). CONCLUSIONS: Women undergoing cardiac surgery are more likely than men to suffer new perioperative neurological events, and they have higher 30-day mortality when these complications occur. The higher incidence of perioperative neurological complications in women cannot be explained by currently known risk factors.


Assuntos
Encefalopatias/epidemiologia , Procedimentos Cirúrgicos Cardíacos , Complicações Pós-Operatórias/epidemiologia , Adulto , Idoso , Dano Encefálico Crônico/epidemiologia , Dano Encefálico Crônico/etiologia , Encefalopatias/etiologia , Procedimentos Cirúrgicos Cardíacos/mortalidade , Procedimentos Cirúrgicos Cardíacos/estatística & dados numéricos , Coma/epidemiologia , Coma/etiologia , Comorbidade , Diabetes Mellitus/epidemiologia , Feminino , Humanos , Hipertensão/epidemiologia , Ataque Isquêmico Transitório/epidemiologia , Ataque Isquêmico Transitório/etiologia , Tempo de Internação/estatística & dados numéricos , Masculino , Pessoa de Meia-Idade , Fatores de Risco , Fatores Sexuais , Acidente Vascular Cerebral/epidemiologia , Acidente Vascular Cerebral/etiologia , Estados Unidos/epidemiologia
16.
Appl Environ Microbiol ; 67(4): 1922-34, 2001 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-11282650

RESUMO

The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant (13)C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. (13)C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta-proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong (13)C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant (13)C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.


Assuntos
Archaea/classificação , Sedimentos Geológicos/microbiologia , Metano/metabolismo , Água do Mar/microbiologia , Sulfatos/metabolismo , Bactérias Redutoras de Enxofre/classificação , Anaerobiose , Archaea/genética , Archaea/metabolismo , DNA Ribossômico/análise , DNA Ribossômico/genética , Hibridização in Situ Fluorescente , Lipídeos/análise , Dados de Sequência Molecular , Oxirredução , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Bactérias Redutoras de Enxofre/genética , Bactérias Redutoras de Enxofre/metabolismo
18.
Nature ; 409(6819): 507-10, 2001 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-11206545

RESUMO

The ocean's interior is Earth's largest biome. Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean. But quantitative data on the abundance of specific microbial groups in the deep sea are lacking. Here we report a year-long study of the abundance of two specific archaeal groups (pelagic euryarchaeota and pelagic crenarchaeota) in one of the ocean's largest habitats. Monthly sampling was conducted throughout the water column (surface to 4,750 m) at the Hawai'i Ocean Time-series station. Below the euphotic zone (> 150 m), pelagic crenarchaeota comprised a large fraction of total marine picoplankton, equivalent in cell numbers to bacteria at depths greater than 1,000 m. The fraction of crenarchaeota increased with depth, reaching 39% of total DNA-containing picoplankton detected. The average sum of archaea plus bacteria detected by rRNA-targeted fluorescent probes ranged from 63 to 90% of total cell numbers at all depths throughout our survey. The high proportion of cells containing significant amounts of rRNA suggests that most pelagic deep-sea microorganisms are metabolically active. Furthermore, our results suggest that the global oceans harbour approximately 1.3 x 10(28) archaeal cells, and 3.1 x 10(28) bacterial cells. Our data suggest that pelagic crenarchaeota represent one of the ocean's single most abundant cell types.


Assuntos
Archaea , Archaea/isolamento & purificação , Biologia Marinha , Oceano Pacífico , RNA Arqueal/análise , RNA Ribossômico/análise , Microbiologia da Água
19.
Syst Biol ; 50(4): 470-8, 2001 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-12116647

RESUMO

The microbial way of life spans at least 3.8 billion years of evolution. Microbial organisms are pervasive, ubiquitous, and essential components of all ecosystems. The geochemical composition of Earth's biosphere has been molded largely by microbial activities. Yet, despite the predominance of microbes during the course of life's history, general principles and theory of microbial evolution and ecology are not well developed. Until recently, investigators had no idea how accurately cultivated microorganisms represented overall microbial diversity. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. Free from the biases of culture-based studies, molecular phylogenetic surveys have revealed a vast array of new microbial groups. Many of these new microbes are widespread and abundant among contemporary microbiota and fall within novel divisions that branch deep within the tree of life. The breadth and extent of extant microbial diversity has become much clearer. A remaining challenge for microbial biologists is to better characterize the biological properties of these newly described microbial taxa. This more comprehensive picture will provide much better perspective on the natural history, ecology, and evolution of extant microbial life.


Assuntos
Archaea/genética , Bactérias/genética , Archaea/classificação , Bactérias/classificação , Ecossistema , Microbiologia Ambiental , Variação Genética , Filogenia
20.
J Am Coll Cardiol ; 36(7): 2174-84, 2000 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-11127458

RESUMO

OBJECTIVES: We sought to evaluate the predictive accuracy of four bypass surgery mortality clinical risk models and to examine the extent to which hospitals' risk-adjusted surgical outcomes vary depending on which risk-adjustment method is applied. BACKGROUND: Cardiovascular "report cards" often compare risk-adjusted surgical outcomes; however, it is unclear to what extent the risk-adjustment process itself may affect these metrics. METHODS: As part of the Cooperative Cardiovascular Project's Pilot Revascularization Study, we compared the predictive accuracy of four bypass clinical risk models among 3,654 Medicare patients undergoing surgery at 28 hospitals in Alabama and Iowa. We also compared the agreement in hospital-level risk-adjusted bypass outcome performance ratings depending on which of the four risk models was applied. RESULTS: Although the four risk models had similar discriminatory abilities (C-index, 0.71 to 0.74), certain models tended to overpredict mortality in higher-risk patients. There was high correlation between a hospital's risk-adjusted mortality rates regardless of which of the four models was used (correlation between risk-adjusted rating, 0.93 to 0.97). In contrast, there was limited agreement in which hospitals were identified as "performance outliers" depending on which risk-adjustment model was used and how outlier status was defined. CONCLUSIONS: A hospital's risk-adjusted bypass surgery mortality rating, relative to its peers, was consistent regardless of the risk-adjustment model applied, supporting their use as a means of provider performance feedback. Designation of performance outliers, however, can vary significantly depending on the benchmark and methods used for this determination.


Assuntos
Ponte de Artéria Coronária/mortalidade , Mortalidade Hospitalar , Modelos Estatísticos , Risco Ajustado , Idoso , Benchmarking , Feminino , Hospitais/classificação , Hospitais/estatística & dados numéricos , Humanos , Masculino , Medicare , Pessoa de Meia-Idade , Avaliação de Resultados em Cuidados de Saúde , Estados Unidos/epidemiologia
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