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1.
Artigo em Inglês | MEDLINE | ID: mdl-35960659

RESUMO

A mesophilic sulphate-reducing micro-organism, able to grow chemolithoautotrophically with H2/CO2 (20 : 80) and with elemental iron as a sole electron donor, was isolated from a consortium capable of degrading long-chain paraffins and designated strain DRH4T. Cells were oval shaped often with bright refractile cores and occurred singly or in pairs. The cells formed pili. Strain DRH4T could grow chemolithoautotrophically with H2/CO2 or elemental iron and chemoorganotrophically utilizing a number of organic substrates, such as fatty acids from formate to octanoate (C1-C8). Sulphate and thiosulphate served as terminal electron acceptors, but sulphite and nitrate did not. Optimal growth was observed from 37 to 40 °C and pH from 6.5 to 7.2. Strain DRH4T did not require NaCl for growth and could proliferate under a broad range of salinities from freshwater (1 g l-1 NaCl) to seawater (27 g l-1 NaCl) conditions. The genomic DNA G+C content was 54.46 mol %. Based on 16S rRNA gene sequence analysis. strain DRH4T was distinct from previously described Deltaproteobacteria species exhibiting the closest affiliation to Desulforhabdus amnigena ASRB1T, Syntrophobacterium sulfatireducens TB8106T and Desulfovirga adipica 12016T with 93.35, 93.42 and 92.85 % similarity, respectively. Strain DRH4T showed significant physiological differences with the aforementioned organisms. Based on physiological differences and phylogenetic comparisons, we propose to classify DRH4T as the type strain (=DSM 113 455T=JCM 39 248T) of a novel species of a new genus with the name Desulfoferrobacter suflitae gen. nov., sp. nov.


Assuntos
Deltaproteobacteria , Processos Autotróficos , Técnicas de Tipagem Bacteriana , Composição de Bases , Dióxido de Carbono , DNA Bacteriano/genética , Ácidos Graxos/química , Hidrogênio , Ferro , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio , Sulfatos
2.
Proc Natl Acad Sci U S A ; 114(12): 3085-3090, 2017 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-28265087

RESUMO

Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning-derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.


Assuntos
Aprendizagem Baseada em Problemas/normas , Ciência/educação , Ensino/normas , Humanos , Som , Estudantes , Tecnologia , Universidades/normas
3.
Appl Microbiol Biotechnol ; 101(16): 6517-6529, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28597336

RESUMO

Offshore oil-producing platforms are designed for efficient and cost-effective separation of oil from water. However, design features and operating practices may create conditions that promote the proliferation and spread of biocorrosive microorganisms. The microbial communities and their potential for metal corrosion were characterized for three oil production platforms that varied in their oil-water separation processes, fluid recycling practices, and history of microbially influenced corrosion (MIC). Microbial diversity was evaluated by 16S rRNA gene sequencing, and numbers of total bacteria, archaea, and sulfate-reducing bacteria (SRB) were estimated by qPCR. The rates of 35S sulfate reduction assay (SRA) were measured as a proxy for metal biocorrosion potential. A variety of microorganisms common to oil production facilities were found, but distinct communities were associated with the design of the platform and varied with different locations in the processing stream. Stagnant, lower temperature (<37 °C) sites in all platforms had more SRB and higher SRA compared to samples from sites with higher temperatures and flow rates. However, high (5 mmol L-1) levels of hydrogen sulfide and high numbers (107 mL-1) of SRB were found in only one platform. This platform alone contained large separation tanks with long retention times and recycled fluids from stagnant sites to the beginning of the oil separation train, thus promoting distribution of biocorrosive microorganisms. These findings tell us that tracking microbial sulfate-reducing activity and community composition on off-shore oil production platforms can be used to identify operational practices that inadvertently promote the proliferation, distribution, and activity of biocorrosive microorganisms.


Assuntos
Archaea/crescimento & desenvolvimento , Bactérias/crescimento & desenvolvimento , Incrustação Biológica , Metais/metabolismo , Indústria de Petróleo e Gás , Petróleo/microbiologia , Microbiologia da Água , Archaea/genética , Archaea/metabolismo , Bactérias/genética , Bactérias/metabolismo , Corrosão , Sulfeto de Hidrogênio/análise , Consórcios Microbianos , Indústria de Petróleo e Gás/economia , RNA Ribossômico 16S/genética , Sulfatos/metabolismo
4.
J Ind Microbiol Biotechnol ; 44(2): 167-180, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-28013395

RESUMO

Navy vessels consist of various metal alloys and biofilm accumulation at the metal surface is thought to play a role in influencing metal deterioration. To develop better strategies to monitor and control metallic biofilms, it is necessary to resolve the bacterial composition within the biofilm. This study aimed to determine if differences in electrochemical current could influence the composition of dominant bacteria in a metallic biofilm, and if so, determine the level of resolution using metagenomic amplicon sequencing. Current was generated by creating galvanic couples between cathodes made from stainless steel and anodes made from carbon steel, aluminum, or copper nickel and exposing them in the Delaware Bay. Stainless steel cathodes (SSCs) coupled to aluminum or carbon steel generated a higher mean current (0.39 mA) than that coupled to copper nickel (0.17 mA). Following 3 months of exposure, the bacterial composition of biofilms collected from the SSCs was determined and compared. Dominant bacterial taxa from the two higher current SSCs were different from that of the low-current SSC as determined by DGGE and verified by Illumina DNA-seq analysis. These results demonstrate that electrochemical current could influence the composition of dominant bacteria in metallic biofilms and that amplicon sequencing is sufficient to complement current methods used to study metallic biofilms in marine environments.


Assuntos
Bactérias/isolamento & purificação , Biofilmes , Eletrodos/microbiologia , Água do Mar/microbiologia , Aço Inoxidável , Alumínio/química , Bactérias/classificação , Carbono/química , Clonagem Molecular , Cobre/química , DNA Bacteriano/isolamento & purificação , Biblioteca Gênica , Níquel/química , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de DNA
5.
Environ Microbiol ; 18(8): 2604-19, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27198766

RESUMO

Anaerobic microbial biodegradation of recalcitrant, water-insoluble substrates, such as paraffins, presents unique metabolic challenges. To elucidate this process, a methanogenic consortium capable of mineralizing long-chain n-paraffins (C28 -C50 ) was enriched from San Diego Bay sediment. Analysis of 16S rRNA genes indicated the dominance of Syntrophobacterales (43%) and Methanomicrobiales (26%). Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community members belonging to the bacterial genus Smithella and the archaeal genera Methanoculleus and Methanosaeta. Five contigs encoding homologs of the catalytic subunit of alkylsuccinate synthase (assA) were detected. Additionally, mRNA transcripts for these genes, including a homolog binned within the 'Smithella' sp. SDB genome scaffold, were detected via RT-PCR, implying that paraffins are activated via 'fumarate addition'. Metabolic reconstruction and comparison with genome scaffolds of uncultivated n-alkane degrading 'Smithella' spp. are consistent with the hypothesis that syntrophically growing 'Smithella' spp. may achieve reverse electron transfer by coupling the reoxidation of ETFred to a membrane-bound FeS oxidoreductase functioning as an ETF:menaquinone oxidoreductase. Subsequent electron transfer could proceed via a periplasmic formate dehydrogenase and/or hydrogenase, allowing energetic coupling to hydrogenotrophic methanogens such as Methanoculleus. Ultimately, these data provide fundamental insight into the energy conservation mechanisms that dictate interspecies interactions salient to methanogenic alkane mineralization.


Assuntos
Alcanos/metabolismo , Deltaproteobacteria/metabolismo , Fumaratos/metabolismo , Methanomicrobiales/metabolismo , Parafina/metabolismo , Biodegradação Ambiental , Deltaproteobacteria/classificação , Deltaproteobacteria/genética , Metabolismo Energético/fisiologia , Genoma Arqueal/genética , Genoma Bacteriano/genética , Metagenômica , Methanomicrobiales/classificação , Methanomicrobiales/genética , Oxirredutases/genética , Oxirredutases/metabolismo , Filogenia , RNA Ribossômico 16S/genética
6.
Appl Microbiol Biotechnol ; 98(2): 907-18, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23636692

RESUMO

A model flow cell system was designed to investigate pitting corrosion in pipelines associated with microbial communities. A microbial inoculum producing copious amounts of H2S was enriched from an oil pipeline biofilm sample. Reservoirs containing a nutrient solution and the microbial inoculum were pumped continuously through six flow cells containing mild steel corrosion coupons. Two cells received corrosion inhibitor "A", two received corrosion inhibitor "B", and two ("untreated") received no additional chemicals. Coupons were removed after 1 month and analyzed for corrosion profiles and biofilm microbial communities. Coupons from replicate cells showed a high degree of similarity in pitting parameters and in microbial community profiles, as determined by 16S rRNA gene sequence libraries but differed with treatment regimen, suggesting that the corrosion inhibitors differentially affected microbial species. Viable microbial biomass values were more than 10-fold higher for coupons from flow cells treated with corrosion inhibitors than for coupons from untreated flow cells. The total number of pits >10 mils diameter and maximum pitting rate were significantly correlated with each other and the total number of pits with the estimated abundance of sequences classified as Desulfomicrobium. The maximum pitting rate was significantly correlated with the sum of the estimated abundance of Desulfomicrobium plus Clostridiales, and with the sum of the estimated abundance of Desulfomicrobium plus Betaproteobacteria. The lack of significant correlation with the estimated abundance of Deltaproteobacteria suggests not all Deltaproteobacteria species contribute equally to microbiologically influenced corrosion (MIC) and that it is not sufficient to target one bacterial group when monitoring for MIC.


Assuntos
Bactérias/efeitos dos fármacos , Biota/efeitos dos fármacos , Corrosão , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
7.
Biofouling ; 30(7): 823-35, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25115517

RESUMO

Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed 'cookies,' revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Biofilmes/classificação , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Corrosão , DNA Bacteriano/genética , Indústrias Extrativas e de Processamento , RNA Ribossômico 16S/genética , Aço/química
8.
Environ Sci Technol ; 47(11): 6052-62, 2013 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-23614475

RESUMO

Ultralow sulfur diesel (ULSD) fuel has been integrated into the worldwide fuel infrastructure to help meet a variety of environmental regulations. However, desulfurization alters the properties of diesel fuel in ways that could potentially impact its biological stability. Fuel desulfurization might predispose ULSD to biodeterioration relative to sulfur-rich fuels and in marine systems accelerate rates of sulfate reduction, sulfide production, and carbon steel biocorrosion. To test such prospects, an inoculum from a seawater-compensated ballast tank was amended with fuel from the same ship or with refinery fractions of ULSD, low- (LSD), and high sulfur diesel (HSD) and monitored for sulfate depletion. The rates of sulfate removal in incubations amended with the refinery fuels were elevated relative to the fuel-unamended controls but statistically indistinguishable (∼50 µM SO4/day), but they were found to be roughly twice as fast (∼100 µM SO4/day) when the ship's own diesel was used as a source of carbon and energy. Thus, anaerobic hydrocarbon metabolism likely occurred in these incubations regardless of fuel sulfur content. Microbial community structure from each incubation was also largely independent of the fuel amendment type, based on molecular analysis of 16S rRNA sequences. Two other inocula known to catalyze anaerobic hydrocarbon metabolism showed no differences in fuel-associated sulfate reduction or methanogenesis rates between ULSD, LSD, and HSD. These findings suggest that the stability of diesel is independent of the fuel organosulfur compound status and reasons for the accelerated biocorrosion associated with the use of ULSD should be sought elsewhere.


Assuntos
Gasolina/análise , Consórcios Microbianos/genética , Água do Mar/microbiologia , Aço , Enxofre/análise , Anaerobiose , Biodegradação Ambiental , Corrosão , Hidrocarbonetos/metabolismo , Dados de Sequência Molecular , RNA Ribossômico 16S , Água do Mar/química , Navios , Sulfatos/química , Enxofre/química
9.
Environ Microbiol ; 14(7): 1762-71, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22429327

RESUMO

Two thermophilic archaea, strain PK and strain MG, were isolated from a culture enriched at 80°C from the inner surface material of a hot oil pipeline. Strain PK could ferment complex organic nitrogen sources (e.g. yeast extract, peptone, tryptone) and was able to reduce elemental sulfur (S°), Fe(3+) and Mn(4+) . Phylogenetic analysis revealed that the organism belonged to the order Thermococcales. Incubations of this strain with elemental iron (Fe°) resulted in the abiotic formation of ferrous iron and the accumulation of volatile fatty acids during yeast extract fermentation. The other isolate, strain MG, was a H(2) :CO(2) -utilizing methanogen, phylogenetically affiliated with the genus Methanothermobacter family. Co-cultures of the strains grew as aggregates that produced CH(4) without exogenous H(2) amendment. The co-culture produced the same suite but greater concentrations of fatty acids from yeast extract than did strain PK alone. Thus, the physiological characteristics of organisms both alone and in combination could conceivably contribute to pipeline corrosion. The Thermococcus strain PK could reduce elemental sulfur to sulfide, produce fatty acids and reduce ferric iron. The hydrogenotrophic methanogen strain MG enhanced fatty acid production by fermentative organisms but could not couple the dissolution Fe° with the consumption of water-derived H(2) like other methanogens.


Assuntos
Archaea/metabolismo , Compostos Férricos/metabolismo , Petróleo/microbiologia , Archaea/genética , Técnicas de Cocultura , Corrosão , DNA Arqueal/genética , Ácidos Graxos/biossíntese , Fermentação , Temperatura Alta , Metano/biossíntese , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Biofouling ; 28(5): 465-78, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22594394

RESUMO

Experiments were designed to evaluate the corrosion-related consequences of storing/transporting fatty acid methyl ester (FAME) alternative diesel fuel in contact with natural seawater. Coastal Key West, FL (KW), and Persian Gulf (PG) seawaters, representing an oligotrophic and a more organic- and inorganic mineral-rich environment, respectively, were used in 60 day incubations with unprotected carbon steel. The original microflora of the two seawaters were similar with respect to major taxonomic groups but with markedly different species. After exposure to FAME diesel, the microflora of the waters changed substantially, with Clostridiales (Firmicutes) becoming dominant in both. Despite low numbers of sulphate-reducing bacteria in the original waters and after FAME diesel exposure, sulphide levels and corrosion increased markedly due to microbial sulphide production. Corrosion morphology was in the form of isolated pits surrounded by an intact, passive surface with the deepest pits associated with the fuel/seawater interface in the KW exposure. In the presence of FAME diesel, the highest corrosion rates measured by linear polarization occurred in the KW exposure correlating with significantly higher concentrations of sulphur and chlorine (presumed sulphide and chloride, respectively) in the corrosion products.


Assuntos
Bactérias/classificação , Bactérias/metabolismo , Gasolina/análise , Água do Mar/química , Água do Mar/microbiologia , Aço/química , Sulfetos/metabolismo , Bactérias/genética , Corrosão , Ésteres/metabolismo , Ácidos Graxos/metabolismo , Genes de RNAr , Hidrocarbonetos/metabolismo , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Environ Microbiol ; 13(4): 1078-90, 2011 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21261797

RESUMO

The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies.


Assuntos
Archaea/crescimento & desenvolvimento , Bactérias/crescimento & desenvolvimento , Biofilmes , Petróleo/microbiologia , Filogenia , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Corrosão , DNA Arqueal/genética , DNA Bacteriano/genética , Biblioteca Gênica , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
12.
Appl Microbiol Biotechnol ; 91(4): 1083-93, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21562978

RESUMO

Nine wells producing from six different reservoirs with salinities ranging from 2.1% to 15.9% were surveyed for presence of surface-active compounds and biosurfactant-producing microbes. Degenerate primers were designed to detect the presence of the surfactin/lichenysin (srfA3/licA3) gene involved in lipopeptide biosurfactant production in members of Bacillus subtilis/licheniformis group and the rhlR gene involved in regulation of rhamnolipid production in pseudomonads. Polymerase chain reaction amplification, cloning, and sequencing confirmed the presence of the srfA3/licA3 genes in brines collected from all nine wells. The presence of B. subtilis/licheniformis strains was confirmed by sequencing two other genes commonly used for taxonomic identification of bacteria, gyrA (gyrase A) and the 16S rRNA gene. Neither rhlR nor 16S rRNA gene related to pseudomonads was detected in any of the brines. Intrinsic levels of surface-active compounds in brines were low or not detected, but biosurfactant production could be stimulated by nutrient addition. Supplementation with a known biosurfactant-producing Bacillus strain together with nutrients increased biosurfactant production. The genetic potential to produce lipopeptide biosurfactants (e.g., srfA3/licA3 gene) is prevalent, and nutrient addition stimulated biosurfactant production in brines from diverse reservoirs, suggesting that a biostimulation approach for biosurfactant-mediated oil recovery may be technically feasible.


Assuntos
Bacillus/isolamento & purificação , Bacillus/metabolismo , Microbiologia do Solo , Solo/química , Tensoativos/metabolismo , Bacillus/classificação , Bacillus/genética , Proteínas de Bactérias/genética , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , Oklahoma , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Salinidade , Análise de Sequência de DNA
13.
Microbiol Resour Announc ; 10(11)2021 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-33737364

RESUMO

Here, we report the genome sequence of Clostridium sp. strain P21, isolated from old hay from Stillwater, Oklahoma. This announcement describes the generation and annotation of the 5.6-Mb genomic sequence of strain P21, which will aid in studies targeting genes involved in the enhancement of acid-alcohol production.

14.
Environ Microbiol ; 12(11): 3074-86, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20602630

RESUMO

Petrochemical and geological evidence suggest that petroleum in most reservoirs is anaerobically biodegraded to some extent. However, the conditions for this metabolism and the cultivation of the requisite microorganisms are rarely established. Here, we report on microbial hydrocarbon metabolism in two distinct oilfields on the North Slope of Alaska (designated Fields A and B). Signature anaerobic hydrocarbon metabolites were detected in produced water from the two oilfields offering evidence of in situ biodegradation activity. Rate measurements revealed that sulfate reduction was an important electron accepting process in Field A (6-807 µmol S l(-1) day(-1)), but of lesser consequence in Field B (0.1-10 µmol S l(-1) day(-1)). Correspondingly, enrichments established at 55°C with a variety of hydrocarbon mixtures showed relatively high sulfate consumption but low methane production in Field A incubations, whereas the opposite was true of the Field B enrichments. Repeated transfer of a Field B enrichment showed ongoing methane production in the presence of crude oil that correlated with ≥ 50% depletion of several component hydrocarbons. Molecular-based microbial community analysis of the methanogenic oil-utilizing consortium revealed five bacterial taxa affiliating with the orders Thermotogales, Synergistales, Deferribacterales (two taxa) and Thermoanaerobacterales that have known fermentative or syntrophic capability and one methanogen that is most closely affiliated with uncultured clones in the H(2)-using family Methanobacteriaceae. The findings demonstrate that oilfield-associated microbial assemblages can metabolize crude oil under the thermophilic and anaerobic conditions prevalent in many petroleum reservoirs.


Assuntos
Archaea/genética , Bactérias Anaeróbias/genética , Metano/biossíntese , Consórcios Microbianos , Petróleo , Sulfatos/metabolismo , Alaska , Anaerobiose , Archaea/classificação , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias Anaeróbias/classificação , Bactérias Anaeróbias/isolamento & purificação , Bactérias Anaeróbias/metabolismo , Sequência de Bases , Biodegradação Ambiental , Crescimento Quimioautotrófico , Temperatura Alta , Hidrocarbonetos/metabolismo , Dados de Sequência Molecular , Oxirredução , Petróleo/análise , Petróleo/metabolismo , Petróleo/microbiologia , Filogenia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética
15.
Microbiol Resour Announc ; 9(17)2020 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327521

RESUMO

Anaerobic alkane metabolism is critical in multiple environmental and industrial sectors, including environmental remediation, energy production, refined fuel stability, and biocorrosion. Here, we report the complete gap-closed genome sequence for a model n-alkane-degrading anaerobe, Desulfoglaeba alkanexedens ALDC.

16.
J Microbiol Methods ; 158: 6-13, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30677454

RESUMO

Three replicate seawater samples were collected on three different days, filtered immediately and preserved with one of two guanidinium thiocyanate-based preservatives (DNAzol™ or RNA Lysis Buffer™ plus ß-mercaptoethanol (RLA+)) and were kept frozen while being shipped to a lab. In parallel, a carboy of seawater was collected on each of the three days and maintained at ambient temperature while being shipped to a lab. Upon receipt the samples were filtered and treated in the same manner as for immediate preservation. Significantly more DNA was obtained from samples immediately preserved with DNAzol than the corresponding shipped samples for 2 of the 3 days. More DNA was extracted from DNAzol preserved samples but more RNA was obtained from RLA+ preserved samples. A protocol was designed to extract both DNA and RNA from split samples preserved with RLA+ and cDNA was synthesized from the RNA. Three high-throughput 16S rRNA gene libraries were constructed, one from DNA preserved with DNAzol, one from DNA preserved with RLA+ and one from cDNA (RLA+ preserved). Greater alpha diversity was found for libraries constructed from immediately preserved vs. shipped samples for both preservation types, with immediate preservation with DNAzol obtaining the highest level of diversity. Libraries constructed from immediately preserved (RLA+) DNA had greater alpha diversity than libraries constructed from shipped preserved (RLA+) DNA or cDNA. Unifrac measures of beta diversity showed clearer separation of sample types and a greater % variance explained for weighted than for unweighted principal coordinate analysis (PCoA) plots, indicating sample types varied more in their relative abundance of taxa than the presence/absence of particular taxa. We recommend immediate preservation of seawater samples, with DNAzol as the preferred preservative if quantification via qPCR will be performed or the highest alpha diversity is desired but preservation with RLA+ if RNA will be extracted.


Assuntos
DNA Bacteriano/isolamento & purificação , Preservação Biológica/métodos , RNA Ribossômico 16S/isolamento & purificação , Manejo de Espécimes/métodos , Archaea/classificação , Bactérias/classificação , Biodiversidade , Variação Genética , Água do Mar/microbiologia , Análise de Sequência de DNA
17.
FEMS Microbiol Ecol ; 95(8)2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31281924

RESUMO

Community compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations were examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ∼92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner microorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical and electrical microbially influenced iron corrosion.


Assuntos
Deltaproteobacteria/metabolismo , Desulfovibrio/metabolismo , Ferro/metabolismo , Parafina/metabolismo , Aço/química , Anaerobiose/fisiologia , Corrosão , Consórcios Microbianos/fisiologia , Oxirredução , Sulfatos/metabolismo
18.
Appl Environ Microbiol ; 74(10): 3022-9, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18378655

RESUMO

World requirements for fossil energy are expected to grow by more than 50% within the next 25 years, despite advances in alternative technologies. Since conventional production methods retrieve only about one-third of the oil in place, either large new fields or innovative strategies for recovering energy resources from existing fields are needed to meet the burgeoning demand. The anaerobic biodegradation of n-alkanes to methane gas has now been documented in a few studies, and it was speculated that this process might be useful for recovering energy from existing petroleum reservoirs. We found that residual oil entrained in a marginal sandstone reservoir core could be converted to methane, a key component of natural gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates ranged from 0.15 to 0.40 micromol/day/g core (or 11 to 31 micromol/day/g oil), with yields of up to 3 mmol CH(4)/g residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed that alkanes were preferentially metabolized. The consortium was found to produce comparable amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic, and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens. Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources.


Assuntos
Archaea/metabolismo , Bactérias/metabolismo , Metano/metabolismo , Óleos/metabolismo , Microbiologia do Solo , Alcanos/metabolismo , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Clonagem Molecular , DNA Arqueal/química , DNA Arqueal/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfatos/metabolismo
19.
J Microbiol Methods ; 150: 55-60, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29803719

RESUMO

Microbially influenced corrosion (MIC), also known as biocorrosion, has significant impacts on the environment and economy. Typical systems to study biocorrosion are either dynamic (once-through flow) or static (serum bottle incubations). Dynamic systems can be materials and personnel intensive, while static systems quickly become nutrient limiting and exhibit long incubations. A semi-continuous biocorrosion cell was developed to address these issues. Low carbon shim steel was used as a test surface. Initial results revealed that 50 ppm glutaraldehyde (GLT), a common oil field biocide, in an abiotic cell was 3.6 times more corrosive (24.5 × 10-3 mm/y) than a biocorrosion cell inoculated with a sulfate-reducing bacteria (SRB) enrichment (6.73 × 10-3 mm/y). The SRB inoculated cell treated with GLT (50 ppm) reduced the corrosion rate from 6.73 × 10-3 mm/y to 3.68 × 10-3 mm/y. It was hypothesized that a biocide-surfactant combination would enhance biocide activity, thereby lowering corrosion in a semi-continuous biocorrosion cell. The biocide and surfactant were GLT (30 ppm) and Tween 80 (TW80; 100 ppm). MIC of SRB increased in the presence of a non-inhibitory concentration of GLT (23.4 × 10-3 mm/y), compared to the untreated +SRB condition (8.29 × 10-3 mm/y). The non-ionic surfactant alone reduced MIC (4.57 × 10-3 mm/y) and even more so in combination with GLT (3.69 × 10-3 mm/y). Over 50% of 16S rDNA sequences in the biofilm on the test surface were identified as belonging to the genera Desulfovibrio and Desulfomicrobium. The utility of a semi-continuous system for MIC studies and biocide testing was demonstrated. The concept of regular partial medium replacement is applicable to different corrosion cell and corrosion coupon geometries. Biocide-surfactant combinations may have the potential to reduce the concentration of biocides used in the field. In addition, a semi-defined medium for enumerating Acid-Producing Bacteria (APB) was developed, resulting in higher recoveries compared to a standard phenol red medium (e.g., 1.1 × 104 APB/cm2 vs < 4 × 10-1 APB/cm2).


Assuntos
Bactérias/efeitos dos fármacos , Biofilmes/efeitos dos fármacos , Desinfetantes/farmacologia , Glutaral/farmacologia , Bactérias Redutoras de Enxofre/efeitos dos fármacos , Ácidos/metabolismo , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Biofilmes/crescimento & desenvolvimento , Carbono , Corrosão , DNA Ribossômico/genética , Concentração de Íons de Hidrogênio , Testes de Sensibilidade Microbiana , Viabilidade Microbiana , Oxirredução , Aço/química , Sulfatos/metabolismo , Sulfetos , Propriedades de Superfície
20.
Chemosphere ; 195: 427-436, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29274988

RESUMO

Fuel biodegradation linked to sulfate reduction can lead to corrosion of the metallic infrastructure in a variety of marine environments. However, the biological stability of emerging biofuels and their potential impact on copper-nickel alloys commonly used in marine systems has not been well documented. Two potential naval biofuels (Camelina-JP5 and Fisher-Tropsch-F76) and their petroleum-derived counterparts (JP5 and F76) were critically assessed in seawater/sediment incubations containing a metal coupon (70/30 Cu-Ni alloy). Relative to a fuel-unamended control (1.2 ±â€¯0.4 µM/d), Camelina-JP5 (86.4 ±â€¯1.6 µM/d) and JP5 (77.6 ±â€¯8.3 µM/d) stimulated much higher rates of sulfate reduction than either FT-F76 (11.4 ±â€¯2.7 µM/d) or F76 (38.4 ±â€¯3.7 µM/d). The general corrosion rate (r2 = 0.91) and pitting corrosion (r2 = 0.92) correlated with sulfate loss in these incubations. Despite differences in microbial community structure on the metal or in the aqueous or sediment phases, sulfate reducing bacteria affiliated with Desulfarculaceae and Desulfobacteraceae became predominant upon fuel amendment. The identification of alkylsuccinates and alkylbenzylsuccinates attested to anaerobic metabolism of fuel hydrocarbons. Sequences related to Desulfobulbaceae were highly enriched (34.2-64.8%) on the Cu-Ni metal surface, regardless of whether the incubation received a fuel amendment. These results demonstrate that the anaerobic metabolism of biofuel linked to sulfate reduction can exacerbate the corrosion of Cu-Ni alloys. Given the relative lability of Camelina-JP5, particular precaution should be taken when incorporating this hydroprocessed biofuel into marine environments serviced by a Cu-Ni metallic infrastructure.


Assuntos
Ligas/química , Biocombustíveis/microbiologia , Cobre/química , Níquel/química , Água do Mar/química , Anaerobiose , Biodegradação Ambiental , Corrosão , Hidrocarbonetos/metabolismo , Sulfatos/metabolismo
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