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Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

Peck V, Quiza L, Buffet JP, Khdhiri M, Durand AA, Paquette A, Thiffault N, Messier C, Beaulieu N, Guertin C, Constant P - Microb Biotechnol (2016)

Bottom Line: Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots.However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest.According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level.

View Article: PubMed Central - PubMed

Affiliation: INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7.

No MeSH data available.


Related in: MedlinePlus

Identification of soil multifunctional molecular indicators. The heatmap shows the absolute abundance of OTUs detected in the soil samples categorized into the four multifunctional classes previously defined (Fig. 2A). Colour bars show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). Taxonomic assignation of the OTU was done using the Greengene reference database V13_8_99 (McDonald et al., 2012). Representative indicators are highlighted with bold characters and are identified with an arrow and asterisk (← *).
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mbt212348-fig-0004: Identification of soil multifunctional molecular indicators. The heatmap shows the absolute abundance of OTUs detected in the soil samples categorized into the four multifunctional classes previously defined (Fig. 2A). Colour bars show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). Taxonomic assignation of the OTU was done using the Greengene reference database V13_8_99 (McDonald et al., 2012). Representative indicators are highlighted with bold characters and are identified with an arrow and asterisk (← *).

Mentions: Comparison of soil samples according to their 16S rRNA gene profile. (A) UPGMA agglomerative clustering of soil samples derived from a matrix of Euclidean distance calculated after Hellinger transformation of OTU (97% identity threshold) absolute abundance. The grey circles denote the nodes delineating the four groups of samples significantly discriminated by SIMPROF permutation procedure (P < 0.05). The scale bar represents the Euclidean distance in the dendrogram. Colour labels show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). (B) Parsimonious RDA triplot of Hellinger‐transformed OTU absolute frequency matrix explained by soil pH and C:N ratio. Only the 14 OTUs displaying extreme distribution in the reduced space are depicted for clarity. These OTUs are identified in the legend with colour bars discriminating α‐Proteobacteria (black), β‐Proteobacteria (blue), δ‐Proteobacteria (red) and other phyla (orange), as determined using the Greengene reference database V13_8_99 (McDonald et al., 2012). The colour labels used to present soil samples in the RDA triplot correspond to the clusters identified in the UPGMA (Fig. 4A). The sample M‐A is absent due the low yield of the DNA extraction procedure for this soil (see the Material and Methods section for more details).


Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

Peck V, Quiza L, Buffet JP, Khdhiri M, Durand AA, Paquette A, Thiffault N, Messier C, Beaulieu N, Guertin C, Constant P - Microb Biotechnol (2016)

Identification of soil multifunctional molecular indicators. The heatmap shows the absolute abundance of OTUs detected in the soil samples categorized into the four multifunctional classes previously defined (Fig. 2A). Colour bars show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). Taxonomic assignation of the OTU was done using the Greengene reference database V13_8_99 (McDonald et al., 2012). Representative indicators are highlighted with bold characters and are identified with an arrow and asterisk (← *).
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835570&req=5

mbt212348-fig-0004: Identification of soil multifunctional molecular indicators. The heatmap shows the absolute abundance of OTUs detected in the soil samples categorized into the four multifunctional classes previously defined (Fig. 2A). Colour bars show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). Taxonomic assignation of the OTU was done using the Greengene reference database V13_8_99 (McDonald et al., 2012). Representative indicators are highlighted with bold characters and are identified with an arrow and asterisk (← *).
Mentions: Comparison of soil samples according to their 16S rRNA gene profile. (A) UPGMA agglomerative clustering of soil samples derived from a matrix of Euclidean distance calculated after Hellinger transformation of OTU (97% identity threshold) absolute abundance. The grey circles denote the nodes delineating the four groups of samples significantly discriminated by SIMPROF permutation procedure (P < 0.05). The scale bar represents the Euclidean distance in the dendrogram. Colour labels show the assignation of the soil samples to their multifunctional class (red; class I, green; class II, blue; class II and black; class IV). (B) Parsimonious RDA triplot of Hellinger‐transformed OTU absolute frequency matrix explained by soil pH and C:N ratio. Only the 14 OTUs displaying extreme distribution in the reduced space are depicted for clarity. These OTUs are identified in the legend with colour bars discriminating α‐Proteobacteria (black), β‐Proteobacteria (blue), δ‐Proteobacteria (red) and other phyla (orange), as determined using the Greengene reference database V13_8_99 (McDonald et al., 2012). The colour labels used to present soil samples in the RDA triplot correspond to the clusters identified in the UPGMA (Fig. 4A). The sample M‐A is absent due the low yield of the DNA extraction procedure for this soil (see the Material and Methods section for more details).

Bottom Line: Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots.However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest.According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level.

View Article: PubMed Central - PubMed

Affiliation: INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7.

No MeSH data available.


Related in: MedlinePlus