Biochemical and molecular biological diversity of soils from three Arctic communities

NRC publication: Ye

Soil microbial population shifts in response to contamination with the explosive RDX

NRC publication: Ye

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

NRC publication: Ye

Effect of experimental contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine on soil bacterial communities

The effect of contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on an indigenous soil bacterial community was examined in two uncontaminated loam soil columns possessing native grasses. One column was spiked twice with RDX crystals for a total RDX load of 1000 mg (kg soil)-1. The reduced metabolite of RDX degradation, hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine, was observed in the column leachate, suggesting anaerobic degradation of RDX. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA from both contaminated and uncontaminated columns produced identical banding patterns which were stable over the course of the experimental period. The bacterial diversity remained high in the contaminated column, as determined by restriction fragment length polymorphism and rarefaction analyses of random 16S rDNA clones. These combined results suggested that long-term exposure to 1000 mg RDX (kg soil)-1 did not produce an observable effect on bacterial diversity or the numerically dominant members of the indigenous soil bacterial community. (c) Biosciences Information Services.NRC publication: Ye

Biochemical and molecular biological diversity of soils from three Arctic communities

NRC publication: Ye

Denitrification in artic soils: Activities and PCR detection of denitrification genes (48th Annual Meeting of the Canadian Society of Microbiologists, Guelph, Ontario, June 14-17)

NRC publication: Ye

Phylogenetic analysis of bacterial communities in the shrimp and sea cucumber aquaculture environment in northern China by culturing and PCR-DGGE

In this study, we investigated the bacterial communities in the shrimp and sea cucumber culture environment, including shrimp ponds (SP), sea cucumber ponds (SCP), mixed-culture ponds (MCP) and the effluent channel (EC) in Qingdao, China. Bacteria cultivation showed that the counts of heterotrophic, nitrate-reducing and sulfate-reducing bacteria in the sediment of SP were higher than that in the sediment of SCP and MCP, varying between 8.7 7 10[4] and 1.86 7 10[6], 2.1 7 10[4] and 1.1 7 10[5], and 9.3 7 10[1] and 1.1 7 10[4] CFU g-1, respectively. In contrast, the counts of ammonium-oxidizing and nitrifying bacteria in the sediment of SP was lower than that in the sediment of SCP and MCP. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA gene and dendrogram analyses showed that bacterial diversity in the mixed-culture environment was higher than that in the monocultures. The similarity of bacterial community between EC and SCP or MCP was higher than that between EC and SP. These results indicated that sea cucumber culture played a significant role in influencing the environmental bacterial communities that were composed mainly of Flavobacteriaceae (64.3%), Bacteriodetes (21%) and delta proteobacteria (14.7%), including the genera of Croceimarina, Lutibacter, Psychroserpens and so on. The results explained the benefit of sea cucumber culture in shrimp ponds at the level of microbial ecology.Dans la pr\ue9sente \ue9tude, nous avons examin\ue9 les communaut\ue9s bact\ue9riennes de milieux d\u2019aquaculture de crevettes et d'holothuries, dont des \ue9tangs d\u2019aquaculture de crevettes (EAC), des \ue9tangs d\u2019aquaculture d\u2019holothuries (EAH), des \ue9tangs d\u2019aquaculture mixte (EAM) et leur canal effluent (CE), \ue0 Qingdao (Chine). La culture des bact\ue9ries montre que le d\ue9compte des bact\ue9ries h\ue9t\ue9rotrophes, r\ue9ductrices de nitrate et sulfator\ue9ductrices dans le s\ue9diment des EAC est plus \ue9lev\ue9 que dans celui des EAH et des EAM, variant de 8,7 7 10[4] \ue0 1,86 7 10[6], de 2,1 7 10[4] \ue0 1,1 7 10[5] et de 9,3 7 10[1] \ue0 1,1 7 10[4] CFU/g, respectivement. En revanche, le d\ue9compte des bact\ue9ries oxydantes de l\u2019ammonium et nitrifiantes dans le s\ue9diment des EAC est plus faible que dans celui des EAH et des EAM. L\u2019\ue9lectrophor\ue8se en gel de gradient d\ue9naturant (DGGE) [denaturing gradient gel electrophoresis] du g\ue8ne de l\u2019ADNr 16S et l\u2019analyse des dendrogrammes montrent que la diversit\ue9 bact\ue9rienne dans le milieu d\u2019aquaculture mixte est plus grande que dans les monocultures. Il existe une similitude plus grande de la communaut\ue9 bact\ue9rienne entre les CE et les EAH ou les EAM qu\u2019entre les CE et les EAC. Ces r\ue9sultats indiquent que la culture des holothuries joue un r\uf4le d\u2019influence important sur les communaut\ue9s bact\ue9riennes du milieu, compos\ue9es principalement de Flavobacteriaceae (64,3 %), de Bacteriodetes (21 %) et de prot\ue9obact\ue9ries delta (14,7 %), y compris les genres Croceimarina, Lutibacter, Psychroserpens et ainsi de suite. Ces r\ue9sultats expliquent l\u2019avantage de pratiquer la culture d\u2019holothuries dans les \ue9tangs d\u2019aquaculture de crevettes sur le plan de l\u2019\ue9cologie microbienne.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