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Explores the presence of Bacteria spp. and Archaea spp. in gas hydrates from the Gulf of Mexico. Indication of microbial consumption of methane or propane in some samples; Assessment of the composition of the microbial community; Determination of total direct counts of hydrate-associated sediments.

We previously described a new method, bacterial chromosomal painting (BCP), for the in situ identification of bacterial cells. Here, we describe the application of this technique to study the ecology and physiology of cultured marine pelagic bacteria from the western Sargasso Sea (WSS). A total of 86 bacteria were isolated from seawater collected from near the surface, at a depth of 250 m and from nutrient-amended seawater incubations. The 10 bacterial isolates that were best represented in environmental genomic DNA from the WSS were selected using reverse genome probing. BCP hybridization cell counts were used to determine the depth-specific distribution of one of the alpha proteobacterial isolates, B5-6, in the WSS during two thermal stratification regimes: stratified and partially mixed. The maximum cell count measured for B5-6 at the summer deep chlorophyll maximum was approximately 4% of the total cell count. This study is the first application of BCP to natural environments. [ABSTRACT FROM AUTHOR]

Identifies bacterial cells by chromosomal painting. Cell collection and fixation; Purified genomic DNA labeling; Sizes of the labeled fragments; Distinction between species and classes; Necessity for lysozyme treatment; Enhancement of signal strength; Applications of bacterial chromosomal painting in microbiology.

Summary: The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure and functional potentials under FPW exposure across a range of concentrations, exposure time and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW‐exposed soils than in FPW‐unexposed soils, with metagenome‐assembled genomes (e.g. Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure and highlight the site‐specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions. [ABSTRACT FROM AUTHOR]

Large-scale mining for oil extraction in the boreal forests of Northern Alberta has led to a disturbance footprint of ~900 km2 of land; which must be reclaimed to equivalent land capabilities. Microorganisms are sensitive to anthropogenic disturbances and play an essential role in the cycling of soil nutrients and plant growth, making them potential indicators of ecosystem function. Thus, the objective of this work was to determine the impact of land reclamation on the composition and function of soil microbial communities in the Athabasca Oil Sands Region (AOSR). We evaluated bacterial community composition via high throughput sequencing of 16S rRNA genes and soil functional diversity by community-level physiological profiling (CLPP). The ranges of variability for these factors observed in soils reclaimed with either peat-mineral mix (PMM), forest floor-mineral mix (FFM), or FFM diluted with sand (Sand-FFM), were compared to that of undisturbed reference soils (NS) and a vegetation removed soil (VR). Differences between reclamation soils and natural soils were clearly discernible, with reclamation imposing a more drastic disturbance to the boreal forest than that of removal of vegetation alone. VR changed the structure of the soil microbial community and increased the overall diversity, within-community interactions, and heterogeneity; while reclamation shifted the microbial community structure to an even greater extent, placing it outside the range of natural variability. Among reclamation substrates, FFM showed the highest level of similarity to the range of natural variability and PMM showed the least. Altogether, our findings underscore the profound impact of anthropogenic activities associated with large-scale mining on soil biological activity, microbial communities, and edaphic profiles. These alterations are of such magnitude that they render the affected soils significant divergent from the reference undisturbed boreal forest soil. [ABSTRACT FROM AUTHOR]

We evaluated above- and belowground ecosystem changes in a 16 year, combined fertilization and warming experiment in a High Arctic tundra deciduous shrub heath (Alexandra Fiord, Ellesmere Island, NU, Canada). Soil emissions of the three key greenhouse gases (GHGs) (carbon dioxide, methane, and nitrous oxide) were measured in mid-July 2009 using soil respiration chambers attached to a FTIR system. Soil chemical and biochemical properties including Q10 values for CO2, CH4, and N2O, Bacteria and Archaea assemblage composition, and the diversity and prevalence of key nitrogen cycling genes including bacterial amoA, crenarchaeal amoA, and nosZ were measured. Warming and fertilization caused strong increases in plant community cover and height but had limited effects on GHG fluxes and no substantial effect on soil chemistry or biochemistry. Similarly, there was a surprising lack of directional shifts in the soil microbial community as a whole or any change at all in microbial functional groups associated with CH4 consumption or N2O cycling in any treatment. Thus, it appears that while warming and increased nutrient availability have strongly affected the plant community over the last 16 years, the belowground ecosystem has not yet responded. This resistance of the soil ecosystem has resulted in limited changes in GHG fluxes in response to the experimental treatments. [ABSTRACT FROM AUTHOR]

Viable microbes have been detected beneath several geographically distant glaciers underlain by different lithologies, but comparisons of their microbial communities have not previously been made. This study compared the microbial community compositions of samples from two glaciers overlying differing bedrock. Bulk meltwater chemistry indicates that sulfide oxidation and carbonate dissolution account for 90% of the solute flux from Bench Glacier, Alaska, whereas gypsum/anhydrite and carbonate dissolution accounts for the majority of the flux from John Evans Glacier, Ellesmere Island, Nunavut, Canada. The microbial communities were examined using two techniques: clone libraries and dot blot hybridization of 16S rRNA genes. Two hundred twenty-seven clones containing amplified 16S rRNA genes were prepared from subglacial samples, and the gene sequences were analyzed phylogenetically. Although some phylogenetic groups, including the Betaproteobacteria, were abundant in clone libraries from both glaciers, other well-represented groups were found at only one glacier. Group-specific oligonucleotide probes were developed for two phylogenetic clusters that were of particular interest because of their abundance or inferred biochemical capabilities. These probes were used in quantitative dot blot hybridization assays with a range of samples from the two glaciers. In addition to shared phyla at both glaciers, each glacier also harbored a subglacial microbial population that correlated with the observed aqueous geochemistry. These results are consistent with the hypothesis that microbial activity is an important contributor to the solute flux from glaciers. [ABSTRACT FROM AUTHOR]

Presents research which studied microzones in the permanent ice covers of Antarctic lakes in the McMurdo Dry Valleys. Source of liquid water inclusions; Microbial consortium among ice sediment particles; Life capabilities of the consortium.

The response of microbial communities to releases of hydraulic fracturing flowback and produced water (PW) may influence ecosystem functions. However, knowledge of the effects of PW spills on freshwater microbiota is limited. Here, we conducted two separate experiments: 16S rRNA gene sequencing combined with random forests modelling was used to assess freshwater community changes in simulated PW spills by volume from 0.05% to 50%. In a separate experiment, live/dead cell viability in a freshwater community was tested during exposure to 10% PW by volume. Three distinct patterns of microbial community shifts were identified: (i) indigenous freshwater genera remained dominant in <2.5% PW, (ii) from 2.5% to 5% PW, potential PW organic degraders such as Pseudomonas , Rheinheimera and Brevundimonas became dominant, and (iii) no significant change in the relative abundance of taxa was observed in >5% PW. Microbial taxa including less abundant genera such as Cellvibrio were potential bioindicators for the degree of contamination with PW. Additionally, live cells were quickly damaged by adding 10% PW, but cell counts recovered in the following days. Our study shows that the responses of freshwater microbiota vary by spill size, and these responses show promise as effective fingerprints for PW spills in aquatic environments. [ABSTRACT FROM AUTHOR]