Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Molecular microbiological evaluation of passive ultrasonic activation as a supplementary disinfecting step: a clinical study.

INTRODUCTION: This in vivo study used molecular microbiology methods to evaluate the effects of passive ultrasonic irrigation (PUI) as a supplementary disinfecting step after root canal preparation. METHODS: Samples were taken from 10 necrotic root canals of teeth with apical periodontitis before (S1) and after rotary nickel-titanium instrumentation using 2.5% NaOCl as the irrigant (S2) and then after PUI for NaOCl activation (S3). The parameters examined included the incidence of positive broad-range polymerase chain reaction (PCR) results for bacterial presence, the impact on bacterial diversity evaluated by PCR-denaturing gradient gel electrophoresis (DGGE), the quantitative bacterial reduction determined by real-time PCR, and the identification of persistent species by clone library analysis. RESULTS: All S1 samples were positive for bacteria in all tests. Treatment procedures were significantly effective in reducing the incidence of positive results for bacteria, the number of bacterial cells (infectious bioburden), and the bacterial diversity (number of species and abundance). However, the supplementary PUI approach did not succeed in significantly enhancing disinfection beyond that achieved by chemomechanical preparation. Several bacterial species/phylotypes were identified in post-treatment samples that were positive for bacteria. CONCLUSIONS: Findings from this clinical study including a small sample size suggest that PUI can be ineffective in significantly improving disinfection of the main root canal after chemomechanical procedures.

Supplementing the antimicrobial effects of chemomechanical debridement with either passive ultrasonic irrigation or a final rinse with chlorhexidine: a clinical study.

INTRODUCTION: The ability of 2 different approaches to supplement the antimicrobial effects of chemomechanical debridement in infected root canals was compared in vivo. METHODS: Samples from necrotic root canals of teeth with apical periodontitis were taken at the baseline (S1), after preparation with rotary nickel-titanium BioRaCe instruments and 2.5% NaOCl irrigation (S2), and then after either passive ultrasonic irrigation (PUI) for activation of NaOCl (n = 13) or a final rinse with 2% chlorhexidine (CHX) (n = 14) (S3). The incidence of positive culture for bacteria and fungi as well as positive broad-range polymerase chain reaction (PCR) results for bacteria, fungi, and archaea was determined. RESULTS: All S1 samples were positive for bacteria in all methods. Fungi were not detected, and archaea occurred in only one S1 sample. Treatment procedures were significantly effective in reducing the incidence of positive culture and PCR results. Although both supplementary approaches reduced the incidence of positive bacteriologic results when compared with postinstrumentation samples, reduction was not statistically significant (P > .05). There was no significant difference for intergroup comparisons either (P > .05). CONCLUSIONS: Although supplementary disinfection with either PUI or a final rinse with CHX can reduce the number of cases with positive culture and PCR results for bacteria, many cases still remain with detectable bacteria in the main root canal. Research on alternative or supplementary antimicrobial methods or substances should be encouraged.

18S rDNA sequences from microeukaryotes reveal oil indicators in mangrove sediment.

BACKGROUND: Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. CONCLUSIONS/SIGNIFICANCE: We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies.

Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons.

Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon throughout the year were best related to salinity and concentrations of NO (3) (-) , dissolved phosphorus and chlorophyll-a, while changes in BCC between lagoons were best related to salinity and dissolved phosphorus concentration. Salinity has a direct impact on the integrity of the bacterial cell, and it was previously observed that phosphorus is the main limiting nutrient to bacterial growth in these lagoons. Therefore, we conclude that great variations in limnological conditions of coastal lagoons throughout time and space resulted in different BCCs and salinity and nutrient concentration, particularly dissolved phosphorus, are the main limnological factors influencing BCC in these tropical coastal lagoons.

Identification and biodegradation potential of a novel strain of Dietzia cinnamea isolated from a petroleum-contaminated tropical soil.

A bacterial strain, named P4, isolated previously from microcosms containing oil-contaminated soil collected from an environmentally protected area of a tropical Atlantic forest (Biological Reserve of Poço das Antas) located in Brazil was identified as Dietzia cinnamea by morphological, biochemical and genotypic tests. Arabian Light and Marlin oils were both degraded when strain P4 was tested for oil degradation ability in microplates. Total Petroleum Hydrocarbons (TPH) analysis, determined by gas chromatography, showed that strain P4 degraded a wide range of n-alkanes, and also pristane and phytane. Furthermore, this strain was also able to grow in mineral liquid media amended with carbazole, quinoline, naphthalene, toluene, gasoline and diesel as the sole carbon sources. The species D. cinnamea has been previously described with only one representative strain isolated from a perianal swab of a patient with a bone marrow transplant. With the results presented here this species is implicated not only as a human pathogen but also as a potential strain for further studies concerning its role for bioremediation of oil contaminated soil.

Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil.

Sixteen spore forming Gram-positive bacteria were isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. These strains were identified as belonging to the genus Bacillus using classical biochemical techniques and API 50CH kits, and their identity was confirmed by sequencing of part of the 16S rRNA gene. All strains were tested for oil degradation ability in microplates using Arabian Light and Marlin oils and only seven strains showed positive results in both kinds of oils. They were also able to grow in the presence of carbazole, n-hexadecane and polyalphaolefin (PAO), but not in toluene, as the only carbon sources. The production of key enzymes involved with aromatic hydrocarbons biodegradation process by Bacillus strains (catechol 1,2-dioxygenase and catechol 2,3-dioxygenase) was verified spectrophotometrically by detection of cis,cis-muconic acid and 2-hydroxymuconic semialdehyde, and results indicated that the ortho ring cleavage pathway is preferential. Furthermore, polymerase chain reaction (PCR) products were obtained when the DNA of seven Bacillus strains were screened for the presence of catabolic genes encoding alkane monooxygenase, catechol 1,2-dioxygenase, and/or catechol 2,3-dioxygenase. This is the first study on Bacillus strains isolated from an oil reservoir in Brazil.