Biochemical and molecular biological diversity of soils from three Arctic communities

NRC publication: Ye

Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities

NRC publication: Ye

Biochemical and molecular biological diversity of soils from three Arctic communities

NRC publication: Ye

유아에서 관찰된 감람-교-소뇌 위축증 (1 부검례 보고)

Olivopontocerebellar atrophy (OPCA) is a group of neurologic multisystem disorders with some trait of heredity which is characterized clinically by cerebellar ataxia and histologically by widespread neuronal loss in the inferior olives, pons and cerebellar cortex. It is generally acknowledged that the OPCA usually begins at middle or older age of life, although the pediatric age group can also be involved. Recently, we have experienced an autopsy case of 10-month-old boy demonstrating the characteristic features of OPCA. Family history was unavailable as nothing was known except the fact that both parents were in their early thirties. We report this case in view of its ccurrence in such a young age and the first pathologic documentation of this entity in the Korean literature. ; 감람-교-소뇌 위축증(olivopontocerebellar atrophy)은 대부분 중년에 그 증상이 나타나 진행성 운동실조의 증세를 보이며, 병리학적으로는 선택적으로 감람핵, 뇌교 및 소뇌에서 심한 신경세포의 소실과 신경섬유의 탈수초 현상을 보이는 비교적 드문 질환이다. 저자들은 기도내의 이물질 흡입으로 사망한 것으로 여겨지는 10개월된 남아의 부검에서 본 증을 경험하였다. 환아는 사망 수 개월전의 진찰에서 다소 머리가 작았던 것외에 외형상 특기할 소견이 없었으며, 지능의 저하도 없었다. 다만 전반적인 운동실조의 증상을 보여 근긴장이 완아 증후근(floppy infant syndrome)을 의심케 하였다. 부검상 소뇌회가 얇고 그 사이가 넓어진 작은 소뇌를 관찰하였으며, 감람핵의 돌출은 미약하였으며 뇌교도 작았다. 현미경적으로 소뇌, 감람핵 및 뇌교의 전반적인 신경세포의 소실과 신경초의 탈실을 보였다. 특히 소뇌 피질의 과립층과 Purkinje 세포의 소실은 현저하였으나 분자층의 위축은 상대적으로 미약하였다. 소뇌 백질, 특히 피질에 가까운, 신경초에서 유수섬유는 거의 관찰되지 않았다. 뇌교에서는 특징적으로 횡 교-소뇌 섬유(transverse pontocerebellar fiber)는 감소하였으나 종 신경초는 잘 유지되어 있었다. 비록 본 예에서 중추신경계 전반에 대한 검색이 이루어지지 않았으며 자세한 가족력을 알 수 없어 완전한 증례가 될 수는 없으나, 문헌상 이 연령층에서 본 증의 보고가 거의 없으며 특징적인 병리학적 소견을 보여 이를 보고하는 바이다

Alteration of microbial community structure affects diesel biodegradation in an Arctic soil

A wide range of microbial taxa are active in hydrocarbon-contaminated Arctic soils, and many are capable of hydrocarbon metabolism. The most effective hydrocarbon degraders may not naturally dominate following contamination events, so shifts in microbial abundance could potentially increase hydrocarbon biodegradation. In this study, we contaminated an Arctic soil with diesel and used gentamicin and vancomycin to inhibit distinct portions of the microbial community. We measured diesel loss using gas chromatography, bacterial and fungal abundance with qPCR, and assessed bacterial diversity and community composition through Ion Torrent sequencing of 16S rRNA gene amplicons. The combined addition of both antibiotics increased diesel biodegradation significantly relative to the no-antibiotic treatment, despite reduced bacterial and fungal abundance; however, this effect was not observed when nutrients were also added. All treatments produced unique bacterial communities, and both Xanthomonadaceae and Micrococcineae were dominant in the dual antibiotic treatment. The bacterial communities resulting from dual gentamicin and vancomycin addition were similar both with and without nutrients, although nutrient addition produced a much larger fungal population, which may partly explain the differences in biodegradation between these two treatments. These results suggest that the most efficient hydrocarbon-degrading community may not always be promoted naturally in contaminated soils.Peer reviewed: YesNRC publication: Ye

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (for example, nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP), which has successfully stimulated degradation in some contaminated Arctic soils. Bacterial community composition of uncontaminated, diesel-contaminated and diesel+MAP soils was assessed through multiplexed 16S (ribosomal RNA) rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by gas chromatography analysis. Diversity of 16S rRNA gene sequences was reduced by diesel, and more so by the combination of diesel and MAP. Actinobacteria dominated uncontaminated soils with 10 percent organic matter, while Proteobacteria dominated higher-organic matter soils, and this pattern was exaggerated following disturbance. Degradation with and without MAP was predictable by initial bacterial diversity and the abundance of specific assemblages of Betaproteobacteria, respectively. High Betaproteobacteria abundance was positively correlated with high diesel degradation in MAP-treated soils, suggesting this may be an important group to stimulate. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.Peer reviewed: YesNRC publication: Ye

Utilization of Fluorescent Microspheres and a Green Fluorescent Protein-Marked Strain for Assessment of Microbiological Contamination of Permafrost and Ground Ice Core Samples from the Canadian High Arctic

Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-μm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a Pseudomonas strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the gfp marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses

Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments▿

High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation

Numerical Analysis of Grassland Bacterial Community Structure under Different Land Management Regimens by Using 16S Ribosomal DNA Sequence Data and Denaturing Gradient Gel Electrophoresis Banding Patterns

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ∼45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721–1730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total amplification products. Semi-improved grassland soils were analyzed only by DGGE. No differences between communities were detected by calculation of diversity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of individual unimproved and improved grassland DGGE profiles, although considerable spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland samples and had much lower within-group variation. DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate analysis but not by principal-coordinate analysis, using unweighted data (considering only the presence and absence of bands) and weighted data (considering the relative intensity of each band), demonstrated that there were clear differences between grasslands, and the results were not affected by weighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differences between complex microbial communities