Average relative proportions of S cycling gene families and categories detected in microbial biofilm samples from native forest, exotic forest, rural and urban streams.

<p><i>dsrA</i> and <i>dsrB</i>, sulphite reductases; <i>aprA</i>, dissimilatory adenosine-5’ phosphosulphate reductase; <i>sox</i>, sulphite oxidase.</p

Average relative proportions of N cycling gene families and categories detected in microbial biofilm samples from native forest, exotic forest, rural and urban streams.

<p><i>nifH</i>, dinitrogenase reductase; <i>hao</i>, hydroxylamine oxidoreductas; <i>amoA</i>, ammonia monooxygenase; <i>nasA</i>, nitrate reductase; <i>nirA</i> and <i>nirB</i>, nitrite reductases; <i>napA</i>, nitrate reductase; <i>nrfA</i>, c-type cytochrome nitrite reductase; <i>hzo</i>, hydrazine oxidoreductase; <i>narG</i>, nitrate reductase; <i>nirK</i> and <i>nirS</i>, nitrite reductases; <i>norB</i>, nitric oxide reductase; <i>nosZ</i>, nitrous oxide reductase; <i>gdh</i>, glutamate dehydrogenase; <i>ureC</i>, urease.</p

MDS plots based on microbial nutrient cycling and energy metabolism gene assemblages (a) and gene families (b) detected in stream biofilms by Geochip analysis.

<p>The total number of nutrition/energy metabolism genes detected in each sample was standardized between all samples (a), or the number of genes contributing to each of 65 nutrition/energy metabolism gene families was determined for each sample, and the total number of genes standardised between samples (b). Hoteo River and Oakley Creek samples had markedly distinct gene families to other samples resulting in a degenerate MDS plot when included, and have therefore been excluded from (b).</p

Relative proportions of C cycling gene families and categories detected in stream biofilm samples.

<p>Three samples with the most divergent C cycling gene assemblages (Ngakaroa, Hoteo, and Oakley streams) are shown in comparison to typical native forest, urban, exotic forest and rural streams. <i>aclB</i>, ATP citrate lyase; CODH, carbon monoxide dehydrogenase; PCC, propionyl-CoA/acetyl-CoA carboxylase; rubisco, ribulose-1, 5-bisphosphate carboxylase/oxygenase; FTHFS, formyltetrahydrofolate synthetase; <i>mcrA</i>, methyl coenzyme M reductase; <i>pmoA</i>, particulate methane monooxygenase; <i>mmoX</i>, methane monooxygenase; <i>aceA</i>, isocitrate lyase; <i>aceB</i>, malate synthase; <i>amyA</i>, alpha-amylase; <i>amyX</i>, amylopullulanase; <i>apu</i>, amylopullulanase; <i>cda</i>, cyclomaltodextrin dextrin-hydrolase; gluco., glucoamylase; isop., isopullulanase; <i>nplT</i>, neopullulanase; <i>pulA</i>, pullulanase; b-ara., bacterial arabinofuranosidase; f-ara., fungal arabinofuranosidase; mann., mannanase; <i>xylA</i>, xylose isomerase; xylan., xylananse; CDH, cellobiose dehydrogenase; cello., cellobiase; endogl., endoglucanase; exogl., exoglucanase; pect., pectinase; <i>assA</i>, alkylsuccinate synthase; <i>limEH</i>, limonene epoxide hydrolase; <i>lmo</i>, limonene monooxygenase; <i>vanA</i>, vanillate monooxygenase; <i>vdh</i>, vanillin dehydrogenase; acetylgl., acetylglucosaminidase; endoch., endochitinase; exoch., exochitinase; <i>glx</i>, glyoxal oxidase; <i>lip</i>, lignin peroxidase; <i>mnp</i>, manganese peroxidase; <i>lcc</i>, phenol oxidase.</p

Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site-3

<p><b>Copyright information:</b></p><p>Taken from "Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site"</p><p>http://www.biomedcentral.com/1471-2164/8/180</p><p>BMC Genomics 2007;8():180-180.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1924859.</p><p></p>re determined by the neighbor-joining method. 100 bootstrap replicates were used, and values above 50 are shown

The normalized signal intensity of the detected key gens families (A) and the organisms (B) involved in energy transformation process under both c-MFCs and o-MFCs.

<p>The signal intensities were the sum of detected individual gene sequences for each functional gene, averaged among three samples. All data are presented as mean±SE. **<i>p</i><0.05, *<i>p</i><0.10.</p

Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site-0

<p><b>Copyright information:</b></p><p>Taken from "Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site"</p><p>http://www.biomedcentral.com/1471-2164/8/180</p><p>BMC Genomics 2007;8():180-180.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1924859.</p><p></p>(Dch), 6-hydroxycylohex-1-en-1-carbonyl-CoA dehydrogenase (Had), 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase (Oah). Red coloring indicates that the gene was induced during growth by benzoate oxidation. The "?" indicates that no orthologs to known benzoyl-CoA reductases found. Figure adapted from [7]

Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site-7

<p><b>Copyright information:</b></p><p>Taken from "Genomic and microarray analysis of aromatics degradation in and comparison to a isolate from a contaminated field site"</p><p>http://www.biomedcentral.com/1471-2164/8/180</p><p>BMC Genomics 2007;8():180-180.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1924859.</p><p></p> NCBI accession numbers 110599026 – 110599050. Only those genes predicted to be involved in aromatics metabolism are shown in color

PBDE congener products of BDE-209 after 70 days performance by c-MFCs and o-MFCs.

<p>PBDE congener products of BDE-209 after 70 days performance by c-MFCs and o-MFCs.</p

The normalized signal intensity of the detected key gens families involved in aromatic compound degradation (A) and chlorinated solvent remediation (B) under both c-MFCs and o-MFCs.

<p>The signal intensities were the sum of detected individual gene sequences for each functional gene, averaged among three samples. All data are presented as mean±SE. *** <i>p</i><0.001, **<i>p</i><0.05, *<i>p</i><0.10.</p