Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential. Although anaerobic communities were common, cores from oil sands and coal beds had unexpectedly high proportions of aerobic hydrocarbon-degrading bacteria. Likewise, most metagenomes had high proportions of genes for enzymes involved in aerobic hydrocarbon metabolism. Hence, although HREs may have been strictly anaerobic and typically methanogenic for much of their history, this may not hold today for coal beds and for the Alberta oil sands, one of the largest remaining oil reservoirs in the world. This finding may influence strategies to recover energy or chemicals from these HREs by in situ microbial processes.

We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4-8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km 2 ) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH 4 ml À 1 water d. Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via 13 CH 4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy 13 C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase.

Oil sands process-affected water (OSPW), produced by surface-mining of oil sands in Canada, is alkaline and contains high concentrations of salts, metals, naphthenic acids, and polycyclic aromatic compounds (PAHs). Residual hydrocarbon biodegradation occurs naturally, but little is known about the hydrocarbon-degrading microbial communities present in OSPW. In this study, aerobic oxidation of benzene and naphthalene in the surface layer of an oil sands tailings pond were measured. The potential oxidation rates were 4.3 μmol L−1 OSPW d−1 for benzene and 21.4 μmol L−1 OSPW d−1 for naphthalene. To identify benzene and naphthalene-degrading microbial communities, metagenomics was combined with stable isotope probing (SIP), high-throughput sequencing of 16S rRNA gene amplicons, and isolation of microbial strains. SIP using 13C-benzene and 13C-naphthalene detected strains of the genera Methyloversatilis and Zavarzinia as the main benzene degraders, while strains belonging to the family Chromatiaceae and the genus Thauera were the main naphthalene degraders. Metagenomic analysis revealed a diversity of genes encoding oxygenases active against aromatic compounds. Although these genes apparently belonged to many phylogenetically diverse taxa, only a few of these taxa were predominant in the SIP experiments. This suggested that many members of the community are adapted to consuming other aromatic compounds, or are active only under specific conditions. 16S rRNA gene sequence datasets have been submitted to the Sequence Read Archive (SRA) under accession number SRP109130. The Gold Study and Project submission ID number in Joint Genome Institute IMG/M for the metagenome is Gs0047444 and Gp0055765.

Despite the presence of well-documented changes in vegetation and faunal communities at the Pleistocene-Holocene transition, it is unclear whether similar shifts occurred in soil microbes. Recent studies do not show a clear connection between soil parameters and community structure, suggesting permafrost microbiome-climate studies may be unreliable. However, the majority of the permafrost microbial ecological studies have been performed only in either Holocene-or Pleistocene-aged sediments and not on permafrost that formed across the dramatic ecosystem reorganization at the Pleistocene-Holocene transition. In our study, we used permafrost recovered in proximity to the Pleistocene-Holocene transition subsampled under strict sterile conditions developed for ancient DNA studies. Our ordination analyses of microbial community composition based on 16S RNA genes and chemical composition of the soil samples resulted into two distinct clusters based on whether they were of late Pleistocene or Holocene age, while samples within an epoch were more similar than those across the boundary and did not result in age based separation. Between epochs, there was a statistically significant correlation between changes in OTU composition and soil chemical properties, but only Ca and Mn were correlated to OTU composition within Holocene aged samples; furthermore, no chemical parameters were correlated to OTU composition within Pleistocene aged samples. Thus, the results indicate that both soil chemical and microbial parameters are fairly stable until a threshold, driven by climate change in our study, is crossed, after which there is a shift to a new steady state. Modern anthropogenic climate change may lead to similar transitions in state for soil biogeochemical systems and microbial communities in Arctic regions.

Abstract. Ice formed in the subglacial environment can contain some of the highest concentrations of solutes, nutrients, and microbes found in glacier systems, which can be released to downstream freshwater and marine ecosystems and glacier forefields. Despite the potential ecological importance of basal ice, our understanding of its spatial and temporal biogeochemical variability remains limited. We hypothesize that the basal thermal regime of glaciers is a dominant control on subglacial biogeochemistry because it influences the degree to which glaciers mobilize material from the underlying substrate and controls the nature and extent of biogeochemical activity that occurs at glacier beds. Here, we characterize the solutes, nutrients, and microbes found in the basal regions of a cold-based glacier and three polythermal glaciers and compare them to those found in overlying glacier ice of meteoric origin. Compared to meteoric glacier ice, basal ice from polythermal glaciers was consistently enriched in major ions, dissolved organic matter (including a specific fraction of humic-like fluorescent material), and microbes and was occasionally enriched in dissolved phosphorus and reduced nitrogen (NH4+) and in a second dissolved component of humic-like fluorescent material. In contrast, the biogeochemistry of basal ice from the cold-based glacier was remarkably similar to that of meteoric glacier ice. These findings suggest that a glacier's basal thermal regime can play an important role in determining the mix of solutes, nutrients, and microbes that are acquired from subglacial substrates or produced in situ.

<p><strong>Abstract.</strong> Ice formed in the subglacial environment can contain some of the highest concentrations of solutes, nutrients, and microbes found in glacier systems. Upon glacial melt, these materials are released to downstream freshwater and marine ecosystems and glacier forefields. Despite the potential ecological importance of basal ice, our understanding of its biogeochemical characteristics, and their spatial and temporal variability, remains limited. We hypothesize that the basal thermal regime of glaciers is a dominant control on subglacial biogeochemistry because it influences the degree to which glaciers mobilize material from the underlying substrate and controls the nature and extent of biogeochemical activity that occurs at glacier beds. Here, we characterize the solutes, nutrients, and microbes found in the basal regions of a cold-based glacier and three polythermal glaciers and compare them to those found in overlying glacier ice. Compared to its parent glacier ice, basal ice from polythermal glaciers was consistently enriched in major ions, dissolved organic matter (including a specific fraction of humic-like fluorescent material), and microbes, and occasionally enriched in dissolved phosphorus and reduced nitrogen (NH<sub>4</sub><sup>+</sup>) and in a second dissolved component of humic-like fluorescent material. In contrast, the biogeochemistry of basal ice from the cold-based glacier was remarkably similar to that of its parent glacier ice. Although basal ice from the cold-based glacier may have acquired some inorganic and organic nutrients from the underlying substrate, it did not appear to contain significant amounts of either solutes or microbes derived from the glacier bed. These findings suggest that a glacier's basal thermal regime can play an important role in determining the mix of solutes, nutrients, and microbes that are acquired from subglacial substrates and/or produced in situ.</p>

An aerobic methane oxidizing bacterium, designated XLMV4 T , was isolated from the oxic surface layer of an oil sands tailings pond in Alberta, Canada. Strain XLMV4 T is capable of growth on methane and methanol as energy sources. NH 4 Cl and sodium nitrate are nitrogen sources. Cells are Gram-negative, beige to yellow-pigmented, motile (via a single polar flagellum), short rods 2.0-3.3 µm in length and 1.0-1.6 µm in width. A thick capsule is produced. Surface glycoprotein or cup shape proteins typical of the genera Methylococcus, Methylothermus and Methylomicrobium were not observed. Major isoprenoid quinones are Q-8 and Q-7 at an approximate molar ratio of 71 : 22. Major polar lipids are phosphoglycerol and ornithine lipids. Major fatty acids are C 16 : 1 ω8+C 16 : 1 ω7 (34 %), C 16 : 1 ω5 (16 %), and C 18 : 1 ω7 (11 %). Optimum growth is observed at pH 8.0 and 25 °C. The DNA G+C content based on a draft genome sequence is 46.7 mol%. Phylogenetic analysis of 16S rRNA genes and a larger set of conserved genes place strain XLMV4 T within the class Gammaproteobacteria and family Methylococcaceae, most closely related to members of the genera Methylomicrobium and Methylobacter (95.0-97.1 % 16S rRNA gene sequence identity). In silico genomic predictions of DNA-DNA hybridization values of strain XLMV4 T to the nearest phylogenetic neighbours were all below 26 %. On the basis of the data presented, strain XLMV4 T is considered to represent a new genus and species for which the name Methylicorpusculum oleiharenae is proposed. Strain XLMV4 T (=DSMZ DSM 27269=ATCC TSD-186) is the type strain.

25This study aims to act as a methodological guide for contamination monitoring, 26 decontamination, and DNA extraction for peaty and silty permafrost samples with low 27 biomass or difficult to extract DNA. We applied a biological tracer, either only in the 28 field or both in the field and in the lab, via either spraying or painting. Spraying in the 29 field followed by painting in the lab resulted in a uniform layer of the tracer on the core 30 sections. A combination of bleaching, washing, and scraping resulted in complete 31 removal of the tracer leaving sufficient material for DNA extraction, while other widely 32 used decontamination methods did not remove all detectable tracer. In addition, of four 33 widely used commercially available DNA extraction kits, only a modified 34ZymoBIOMICS TM DNA Microprep kit was able to acquire PCR amplifiable DNA. 35Permafrost chemical parameters, age, and soil texture did not have an effect on 36 decontamination efficacy; however, the permafrost type did influence DNA extraction. 37Based on these findings, we developed recommendations for permafrost microbiologists 38 to acquire contaminant-free DNA from permafrost with low biomass. 39 IMPORTANCE: 40Permafrost has the capacity to preserve microbial and non-microbial genomic material for 41 millennia; however, major challenges are associated with permafrost samples, including 42 decontamination of samples and acquiring pure DNA. Contamination of samples during 43 coring and post coring handling and processing could affect downstream analyses and 44 interpretations. Despite the use of multiple different decontamination and DNA extraction 45 methods in studies of permafrost, the efficacy of these methods is not well known. We 46 used a biological tracer to test the efficacy of previously published decontamination 47 methods, as well as a bleach-based method we devised, on two chemically and 48 structurally different permafrost core sections. Our method was the only one that 49 removed all detectable tracer. In addition, we tested multiple DNA extraction kits and 50 modified one that is able to acquire pure, PCR amplifiable DNA from silty, and to some 51 extent from peaty, permafrost samples. 52 53 54 55