Biodegradation of weathered crude oil by microbial communities in solid and melted sea ice.

Abstract Oil spilled in the Arctic may drift into ice-covered areas and become trapped until the ice melts. To determine if exposure to oil during freezing may have a priming effect on degradation of the oil, weathered dispersed oil (2-3 mg/L) was frozen into solid ice for 200 days at -10 °C, then melted and incubated for 64 days at 4 °C. No degradation was measured in oil frozen into ice prior to melting. Both total amount of oil and target compounds were biotransformed by the microbial community from the melted ice. However, oil released from melted ice was degraded at a slower rate than oil incubated in fresh seawater at the same temperature (4 °C), and by a different microbial community. These data suggest negligible biodegradation of oil frozen in sea ice, while oil-degrading bacteria surviving in the ice may contribute to biodegradation when the ice melts

Impact of Intensive Land-Based Fish Culture in Qingdao, China, on the Bacterial Communities in Surrounding Marine Waters and Sediments

The impact of intensive land-based fish culture in Qingdao, China, on the bacterial communities in surrounding marine environment was analyzed. Culture-based studies showed that the highest counts of heterotrophic, ammonium-oxidizing, nitrifying, and nitrate-reducing bacteria were found in fish ponds and the effluent channel, with lower counts in the adjacent marine area and the lowest counts in the samples taken from 500 m off the effluent channel. Denaturing gradient gel electrophoresis (DGGE) analysis was used to assess total bacterial diversity. Fewer bands were observed from the samples taken from near the effluent channel compared with more distant sediment samples, suggesting that excess nutrients from the aquaculture facility may be reducing the diversity of bacterial communities in nearby sediments. Phylogenetic analysis of the sequenced DGGE bands indicated that the bacteria community of fish-culture-associated environments was mainly composed of Flavobacteriaceae, gamma- and deltaproteobacteria, including genera Gelidibacter, Psychroserpen, Lacinutrix, and Croceimarina

Fate of diluted bitumen spilled in the coastal waters of British Columbia, Canada.

Abstract There is public concern about the behaviour of spilled diluted bitumen (dilbit) in marine and estuarine waters. We provide a preliminary assessment of the results of laboratory experiments and models, in the context of environmental conditions in the coastal waters of British Columbia. Most dilbit spilled within this region would likely float at the surface and be transported to shore by winds and currents. Fresh dilbit is too light to sink in coastal waters. Highly weathered dilbit could sink where salinity is less than 14, typically only near river mouths and in the top 1–3 m of fjords after heavy rainfall. Subsurface plumes of weathered dilbit could re-emerge at the surface. Sinking oil-particle aggregates are unlikely to form in coastal waters. However, dilbit could be entrained below the surface by wave mixing during storms and to depths of 150 m by coherent mixing in the Haro Strait tidal convergence zone

The willow microbiome is influenced by soil petroleum-hydrocarbon concentration with plant compartment-specific effects

International audienceThe interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

The fate of the carbon stocked in permafrost following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but no comprehensive study has yet addressed their composition and functional potential in permafrost. Here, a 2-m deep permafrost sample and its overlying active layer soil were subjected to metagenomic sequencing, quantitative PCR (qPCR) and microarray analyses

Life in mine tailings: microbial population structure across the bulk soil, rhizosphere, and roots of boreal species colonizing mine tailings in northwestern Québec

Abstract Purpose Mining activities have negative effects on soil characteristics and can result in low pH, high heavy metal content, and limited levels of essential nutrients. A tailings storage area located in northwestern Québec showed natural colonization by plants from the adjacent natural environment. The objective of the study was to determine the main edaphic parameters that structured microbial populations associated with the indigenous woody plants that had naturally colonized the site. Methods Microbial populations were studied in the bulk soil, the rhizosphere, and inside plant roots using Illumina sequencing, ordination analysis (i.e., redundancy analysis (RDA) and principal coordinates analysis (PCoA)), ternary plotting, and statistical analysis (MANOVA). Results The main variables that drove the microbial community patterns were plant species and the tailings pH. Indeed, the main bacterial classes were Gammaproteobacteria and Deltaproteobacteria in both the rhizosphere and root endosphere. Analysis revealed that some dominant operational taxonomic units (e.g., Pseudomonas sp., Acinetobacter sp., and Delftia sp.) were present in increased proportions in roots for each plant species under study. This study also revealed that many of the most abundant fungal genera (e.g., Claussenomyces, Eupenicillium, and Trichoderma) were more abundant in the rhizosphere than in the root endosphere. Conclusions This comprehensive study of the microbial community dynamics in the bulk soil, rhizosphere, and root endosphere of boreal trees and shrubs could be beneficial in facilitating the rehabilitation of disturbed ecosystems

Comparative Transcriptomics of Cold Growth and Adaptive Features of a Eury- and Steno-Psychrophile

Permafrost subzero environments harbor diverse, active communities of microorganisms. However, our understanding of the subzero growth, metabolisms, and adaptive properties of these microbes remains very limited. We performed transcriptomic analyses on two subzero-growing permafrost isolates with different growth profiles in order to characterize and compare their cold temperature growth and cold-adaptive strategies. The two organisms, Rhodococcus sp. JG3 (-5 to 30°C) and Polaromonas sp. Eur3 1.2.1 (-5 to 22°C), shared several common responses during low temperature growth, including induction of translation and ribosomal processes, upregulation of nutrient transport, increased oxidative and osmotic stress responses, and stimulation of polysaccharide capsule synthesis. Recombination appeared to be an important adaptive strategy for both isolates at low temperatures, likely as a mechanism to increase genetic diversity and the potential for survival in cold systems. While Rhodococcus sp. JG3 favored upregulating iron and amino acid transport, sustaining redox potential, and modulating fatty acid synthesis and composition during growth at -5°C compared to 25°C, Polaromonas sp. Eur3 1.2.1 increased the relative abundance of transcripts involved in primary energy metabolism and the electron transport chain, in addition to signal transduction and peptidoglycan synthesis at 0°C compared to 20°C. The increase in energy metabolism may explain why Polaromonas sp. Eur3 1.2.1 is able to sustain growth rates at 0°C comparable to those at higher temperatures. For Rhodococcus sp. JG3, flexibility in use of carbon sources, iron acquisition, control of membrane fatty acid composition, and modulating redox and co-factor potential may be ways in which this organism is able to sustain growth over a wider range of temperatures. Increasing our understanding of the microbes in these habitats helps us better understand active pathways and metabolisms in extreme environments. Identifying novel, thermolabile, and cold-active enzymes from studies such as this is also of great interest to the biotechnology and food industries

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada’s Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River–Lake St. Clair-Detroit River–Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere

Arctic microbial ecosystems and impacts of extreme warming during the International Polar Year

As a contribution to the International Polar Year program MERGE (Microbiological and Ecological Responses to Global Environmental change in polar regions), studies were conducted on the terrestrial and aquatic microbial ecosystems of northern Canada (details at: http://www.cen.ulaval.ca/merge/). The habitats included permafrost soils, saline coldwater springs, supraglacial lakes on ice shelves, epishelf lakes in fjords, deep meromictic lakes, and shallow lakes, ponds and streams. Microbiological samples from each habitat were analysed by HPLC pigment assays, light and fluorescence microscopy, and DNA sequencing. The results show a remarkably diverse microflora of viruses, Archaea (including ammonium oxidisers and methanotrophs), Bacteria (including filamentous sulfur-oxidisers in a saline spring and benthic mats of Cyanobacteria in many waterbodies), and protists (including microbial eukaryotes in snowbanks and ciliates in ice-dammed lakes). In summer 2008, we recorded extreme warming at Ward Hunt Island and vicinity, the northern limit of the Canadian high Arctic, with air temperatures up to 20.5 \ub0C. This was accompanied by pronounced changes in microbial habitats: deepening of the permafrost active layer; loss of perennial lake ice and sea ice; loss of ice-dammed freshwater lakes; and 23% loss of total ice shelf area, including complete break-up and loss of the Markham Ice Shelf cryo-ecosystem. These observations underscore the vulnerability of Arctic microbial ecosystems to ongoing climate change.Peer reviewed: YesNRC publication: Ye

Arctic microbial ecosystems and impacts of extreme warming during the International Polar Year

As a contribution to the International Polar Year program MERGE (Microbiological and Ecological Responses to Global Environmental change in polar regions), studies were conducted on the terrestrial and aquatic microbial ecosystems of northern Canada (details at: http://www.cen.ulaval.ca/merge/). The habitats included permafrost soils, saline coldwater springs, supraglacial lakes on ice shelves, epishelf lakes in fjords, deep meromictic lakes, and shallow lakes, ponds and streams. Microbiological samples from each habitat were analysed by HPLC pigment assays, light and fluorescence microscopy, and DNA sequencing. The results show a remarkably diverse microflora of viruses, Archaea (including ammonium oxidisers and methanotrophs), Bacteria (including filamentous sulfur-oxidisers in a saline spring and benthic mats of Cyanobacteria in many waterbodies), and protists (including microbial eukaryotes in snowbanks and ciliates in ice-dammed lakes). In summer 2008, we recorded extreme warming at Ward Hunt Island and vicinity, the northern limit of the Canadian high Arctic, with air temperatures up to 20.5 \ub0C. This was accompanied by pronounced changes in microbial habitats: deepening of the permafrost active layer; loss of perennial lake ice and sea ice; loss of ice-dammed freshwater lakes; and 23% loss of total ice shelf area, including complete break-up and loss of the Markham Ice Shelf cryo-ecosystem. These observations underscore the vulnerability of Arctic microbial ecosystems to ongoing climate change.Peer reviewed: YesNRC publication: Ye