<i>Punctularia strigosozonata</i> transcripts with predicted protein functions expressed ≥ log₂(2-fold) (adjusted p < 0.01) in comparisons of 20-day growth on aspen and pine media with and without Bunker C oil.

<p>Positive log₂ fold changes indicate transcript accumulation in the first treatment while negative log₂ fold changes indicate transcript accumulation in the second treatment.</p><p><i>Punctularia strigosozonata</i> transcripts with predicted protein functions expressed ≥ log₂(2-fold) (adjusted p < 0.01) in comparisons of 20-day growth on aspen and pine media with and without Bunker C oil.</p

Degradation (%) of phenanthrene, a C14 alkane, and a C10 alkane in Bunker C oil by white-rot fungi.

<p>Degradation percentages were calculated using <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130381#pone.0130381.e001" target="_blank">Eq 1</a>.</p><p>Degradation (%) of phenanthrene, a C14 alkane, and a C10 alkane in Bunker C oil by white-rot fungi.</p

Biplot of principal components (PC) axes PC1 and PC2 derived from a Principal Components Analysis (PCA) of mapped paired-end Illumina RNA-Seq reads from 20 day-old <i>Punctularia strigosozonata</i> cultures in media treatments (aspen, aspen with Bunker C oil, pine, and pine with Bunker C oil).

<p>Ordination was completed in the R package DESeq.</p

Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation

<div><p>Fungal lignocellulolytic enzymes are promising agents for oxidizing pollutants. This study investigated degradation of Number 6 “Bunker C” fuel oil compounds by the white-rot fungi <i>Irpex lacteus</i>, <i>Trichaptum biforme</i>, <i>Phlebia radiata</i>, <i>Trametes versicolor</i>, and <i>Pleurotus ostreatus</i> (Basidiomycota, Agaricomycetes). Averaging across all studied species, 98.1%, 48.6%, and 76.4% of the initial Bunker C C10 alkane, C14 alkane, and phenanthrene, respectively were degraded after 180 days of fungal growth on pine media. This study also investigated whether Bunker C oil induces changes in gene expression in the white-rot fungus <i>Punctularia strigosozonata</i>, for which a complete reference genome is available. After 20 days of growth, a monokaryon <i>P</i>. <i>strigosozonata</i> strain degraded 99% of the initial C10 alkane in both pine and aspen media but did not affect the amounts of the C14 alkane or phenanthrene. Differential gene expression analysis identified 119 genes with ≥ log₂(2-fold) greater expression in one or more treatment comparisons. Six genes were significantly upregulated in media containing oil; these genes included three enzymes with potential roles in xenobiotic biotransformation. Carbohydrate metabolism genes showing differential expression significantly accumulated transcripts on aspen vs. pine substrates, perhaps reflecting white-rot adaptations to growth on hardwood substrates. The mechanisms by which <i>P</i>. <i>strigosozonata</i> may degrade complex oil compounds remain obscure, but degradation results of the 180-day cultures suggest that diverse white-rot fungi have promise for bioremediation of petroleum fuels.</p></div

Illumina RNA-Seq read counts and percentages of reads mapped to the <i>Punctularia strigosozonata</i> genome and transcriptome.

<p>Illumina RNA-Seq read counts and percentages of reads mapped to the <i>Punctularia strigosozonata</i> genome and transcriptome.</p

Hydrocarbon degradation by <i>Trichaptum biforme</i>.

<p>GC-MS chromatograms of (a) alkane and (b) phenanthrene degradation by <i>T</i>. <i>biforme</i> measured after 180 days of growth in pine media with Bunker C oil. Black lines = <i>T</i>. <i>biforme</i> profiles; blue lines = Bunker C oil profiles.</p

Genes that are outliers in the correspondence analysis of codon usage (red points in Fig. 1).

<p>The assumed cellular location is noted as follows: C, chloroplast minicircles; M, mitochrondrium; N, nucleus. All genes were grouped according to their BLASTX annotation and the number of genes for each annotation is shown for both species. Genes with less than 100 analyzed codons were not included.</p

Comparison of the antioxidant gene repertoire between <i>Arabidopsis thaliana</i>, <i>Phycomitrella patens</i>, <i>Symbiodinium</i> sp. CassKB8, <i>Symbiodinium</i> sp. Mf1.05b, <i>Thalassosira pseudonana</i>, and <i>Phaeodactylum tricornutum</i> based on Pfam domains associated with antioxidant function.

<p>Comparison of the antioxidant gene repertoire between <i>Arabidopsis thaliana</i>, <i>Phycomitrella patens</i>, <i>Symbiodinium</i> sp. CassKB8, <i>Symbiodinium</i> sp. Mf1.05b, <i>Thalassosira pseudonana</i>, and <i>Phaeodactylum tricornutum</i> based on Pfam domains associated with antioxidant function.</p

Comparison of histones and nucleosome-associated proteins from this and previous studies (DinoEST).

*<p>Subtype not specified.</p

Annotation of pathways and complexes in the transcriptome data (values are numbers of genes, i.e. contigs and singlets clustered at 90% similarity).

*<p>COG0096 and COG0552 were not identified.</p