Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities.

Oil sands tailings ponds store the waste slurry generated by extracting bitumen from surface-mined oil (tar) sands ores. The ponds support diverse microbial communities involved in element cycling, greenhouse gas production, and hydrocarbon biodegradation that influence pond management and their environmental footprint. Since previous reports indicate that there are similar microbial metabolic functions amongst ponds, analogous microbiomes may be expected but ponds actually harbour distinct communities. Partial 16S rRNA gene pyrotag sequences from 95 samples were obtained from six ponds managed by three operators. From these we discerned a core prokaryotic microbiome, a subset of microbes shared amongst different samples, defined as operational taxonomic units (OTUs) at the lowest taxonomic level identifiable in individual ponds and pooled pond datatsets. Of the ∼1500-2700 OTUs detected per pond, 4-10 OTUs were shared among ≥75% of the samples per pond, but these few OTUs represented 39-54% of the ponds' sequence reads. Only 2-5 OTUs were shared by the majority of samples from all ponds. Thus the prokaryotic communities within these ponds consist of a few core taxa and numerous accessory members that likely afford resiliency and functional redundancy including roles in iron-, nitrogen- and sulfur-cycling, syntrophy, fermentation, and methanogenesis.

LincRNA-p21 acts as a mediator of ING1b-induced apoptosis.

ING1b is a tumor suppressor that affects transcription, cell cycle control and apoptosis. ING1b is deregulated in disease, and its activity is closely linked to that of p53. In addition to regulating protein-coding genes, we found that ING1b also influences the expression of large intergenic non-coding RNAs (lincRNAs). In particular, lincRNA-p21 was significantly induced after DNA-damage stress or by ING1b overexpression. Furthermore, lincRNA-p21 expression in response to DNA damage was significantly attenuated in cells lacking ING1b. LincRNA-p21 is also a target of p53 and can trigger apoptosis in mouse cell models. We found that this function of lincRNA-p21 is conserved in human cell models. Moreover, ING1b and p53 could function independently to influence lincRNA-p21 expression. However, their effects become more additive under conditions of stress. In particular, ING1b regulates lincRNA-p21 levels by binding to its promoter and is required for induction of lincRNA-p21 by p53. The ability of ING1b to cause apoptosis is also impaired in the absence of lincRNA-p21. Surprisingly, deletion of the ING1b plant homeodomain, which allows it to bind histones and regulate chromatin structure, did not alter regulation of lincRNA-p21. Our findings suggest that ING1b induces lincRNA-p21 expression independently of histone 3 lysine 4 trimethylation mark recognition and that lincRNA-p21 functions downstream of ING1b. Thus, regulation at the level of lincRNA-p21 may represent the point at which ING1b and p53 pathways converge to induce apoptosis under specific stress conditions.

The origin of land plants: phylogenetic relationships among charophytes, bryophytes, and vascular plants inferred from complete small-subunit ribosomal RNA gene sequences.

Complete nuclear-encoded small-subunit 18S rRNA (= SSU rRNA) gene sequences were determined for the prasinophyte green alga Mantoniella squamata; the charophycean green algae Chara foetida, Coleochaete scutata, Klebsormidium flaccidum, and Mougeotia scalaris; the bryophytes Marchantia polymorpha, Fossombronia pusilla, and Funaria hygrometrica; and the lycopod Selaginella galleottii to get a better insight into the sequential evolution from green algae to land plants. The sequences were aligned with several previously published SSU rRNA sequences from chlorophytic and charophytic algae as well as from land plants to infer the evolutionary relationships for major evolutionary lineages within the Chlorobionta by distance matrix, maximum parsimony, and maximum likelihood analyses. Phylogenetic trees created by the different methods consistently placed the Charophyceae on the branch leading to the land plants. The Charophyceae were shown to be polyphyletic with the Charales ("charalean" algae) diverging earlier than the Coleochaetales, Klebsormidiales, Chlorokybales, and Zygnematales ("charophycean" algae) which branch from a point closer to the land plants in most analyses. Maximum parsimony and maximum likelihood analyses imply a successive evolution from "charophycean" algae, particularly Coleochaetales, to bryophytes, lycopods, and seed plants. In contrast, distance matrix methods group the bryophytes together with the "charophycean" algae, suggesting a separate evolution of these organisms compared with the club moss and the seed plants.