Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

Tracing biogeochemical and microbial variability over a complete oil sand mining and recultivation process

Recultivation of disturbed oil sand mining areas is an issue of increasing importance. Nevertheless only little is known about the fate of organic matter, cell abundances and microbial community structures during oil sand processing, tailings management and initial soil development on reclamation sites. Thus the focus of this work is on biogeochemical changes of mined oil sands through the entire process chain until its use as substratum for newly developing soils on reclamation sites. Therefore, oil sand, mature fine tailings (MFTs) from tailings ponds and drying cells and tailings sand covered with peat-mineral mix (PMM) as part of land reclamation were analyzed. The sample set was selected to address the question whether changes in the above-mentioned biogeochemical parameters can be related to oil sand processing or biological processes and how these changes influence microbial activities and soil development. GC-MS analyses of oil-derived biomarkers reveal that these compounds remain unaffected by oil sand processing and biological activity. In contrast, changes in polycyclic aromatic hydrocarbon (PAH) abundance and pattern can be observed along the process chain. Especially naphthalenes, phenanthrenes and chrysenes are altered or absent on reclamation sites. Furthermore, root-bearing horizons on reclamation sites exhibit cell abundances at least ten times higher (10(8) to 10(9) cells g(-1)) than in oil sand and MFT samples (10(7) cells g(-1)) and show a higher diversity in their microbial community structure. Nitrate in the pore water and roots derived from the PMM seem to be the most important stimulants for microbial growth. The combined data show that the observed compositional changes are mostly related to biological activity and the addition of exogenous organic components (PMM), whereas oil extraction, tailings dewatering and compaction do not have significant influences on the evaluated compounds. Microbial community composition remains relatively stable through the entire process chain.

Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8)

We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.

Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment

In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing (SIP) approach. Methanotrophs in lake sediment were labelled using (13)CH4, and both labelled and unlabelled-RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled-RNA metatranscriptome was dominated by methanotroph sequences, particularly from Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.

Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common

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.

Direct evaluation of in situ biodegradation in Athabasca oil sands tailings ponds using natural abundance radiocarbon

Compound-specific stable (δ(13)C) and radiocarbon (Δ(14)C) isotopes of phospholipid fatty acids (PLFAs) were used to evaluate carbon sources utilized by the active microbial populations in surface sediments from Athabasca oil sands tailings ponds. Algal-specific PLFAs were absent at three of the four sites investigated, and δ(13)CPLFA values were generally within ~3‰ of that reported for oil sands bitumen (~-30‰), suggesting that the microbial communities growing on petroleum constituents were dominated by aerobic heterotrophs. Δ(14)CPLFA values ranged from -906 to -586‰ and pointed to significant uptake of fossil carbon, particularly in PLFAs (e.g., cy17:0 and cy19:0) often associated with petroleum hydrocarbon degrading bacteria. The comparatively heavier Δ(14)C values found in other, less specific PLFAs (e.g., 16:0) indicated the preferential uptake of younger organic matter by the general microbial population. Since the main carbon pools in tailings sediment were essentially "radiocarbon dead" (i.e., Δ(14)C ~ -1000‰), the principal source for this relatively modern carbon is considered to be the Athabasca River, which provides the bulk of the water used in the bitumen extraction process. The preferential utilization of the minor amount of younger and presumably more labile material present in systems otherwise dominated by petroleum carbon has important implications for remediation strategies, since it implies that organic contaminants may persist long after reclamation has begun. Alternatively, this young organic matter could play a vital and necessary role in supporting the microbial utilization of fossil carbon via cometabolism or priming processes.

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members

A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6-C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic-fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO(2) fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction.