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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

Multifunctional comparison of soil samples according to their physicochemical (C, N, C:N ratio, pH, texture), trace gas exchanges (H2, CO, CO2) and abundance of bacteria (16S rRNA gene abundance; labelled as ‘Biomass’ in the plot) profiles. (A) UPGMA agglomerative clustering of soil samples according to a Euclidean distance matrix calculated with standardized variables. The grey circles denote the nodes delineating the four multifunctional classes significantly discriminated by SIMPROF permutation procedure (P < 0.05). 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). The scale bar represents the Euclidean distance in the dendrogram. (B) Principal component analysis showing the distribution of sampling sites in a reduced space defined by soil physicochemical properties, gaseous exchanges and abundance of bacteria. The colours used to present soil samples correspond to the clusters identified in the UPGMA (A). (C) Variables defining the distribution of soil samples along the first and the second axis are represented along with the equilibrium circle of descriptors showing the contribution of variables to the formation of the reduced space. The detection limit of the qPCR assay was utilized to estimate the abundance bacteria in sample M‐A for which the low yield of the DNA extraction procedure precluded qPCR and bacterial 16S rRNA gene profiling (see the Material and Methods section for more details).
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mbt212348-fig-0002: Multifunctional comparison of soil samples according to their physicochemical (C, N, C:N ratio, pH, texture), trace gas exchanges (H2, CO, CO2) and abundance of bacteria (16S rRNA gene abundance; labelled as ‘Biomass’ in the plot) profiles. (A) UPGMA agglomerative clustering of soil samples according to a Euclidean distance matrix calculated with standardized variables. The grey circles denote the nodes delineating the four multifunctional classes significantly discriminated by SIMPROF permutation procedure (P < 0.05). 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). The scale bar represents the Euclidean distance in the dendrogram. (B) Principal component analysis showing the distribution of sampling sites in a reduced space defined by soil physicochemical properties, gaseous exchanges and abundance of bacteria. The colours used to present soil samples correspond to the clusters identified in the UPGMA (A). (C) Variables defining the distribution of soil samples along the first and the second axis are represented along with the equilibrium circle of descriptors showing the contribution of variables to the formation of the reduced space. The detection limit of the qPCR assay was utilized to estimate the abundance bacteria in sample M‐A for which the low yield of the DNA extraction procedure precluded qPCR and bacterial 16S rRNA gene profiling (see the Material and Methods section for more details).

Mentions: Soil physicochemical properties, gaseous exchanges and bacteria abundance variables were utilized to define a multifunctional soil classification. Under this classification approach, the distribution of each variable was considered to compute a distance matrix measuring the association between soil samples (Fig. 2A). Four different multifunctional classes were identified in the clustering analysis. The level of disturbance characterizing each class was defined on the basis of their Euclidean distance from the unlogged natural forest plots. Firstly, the soil sample constituting class I (M‐B) represented the MSP treatment that resulted in the most intense disturbance of baseline ecological functions. Secondly, soil samples included in class II (S‐A, S‐B) belong to the category of MSP treatments that caused slight deviations from baseline soil ecological functions. Soil samples belonging to class III (N‐B, N‐A, N‐C) correspond to baseline of soil ecological functions. Finally, class IV (S‐C, I‐A, I‐C, I‐B, M‐A, M‐C, D‐A, D‐B and D‐C) encompass soils for which the MSP treatments caused important alteration of baseline ecological functions at the microsite level. The unlogged natural forest was the sole condition for which replicated composite samples exhibited treatment‐specific, conserved multifunctional profile. Taken together, this classification model indicates that soil multifunctional profile observed in inversion and mound excavations plots were those showing the strongest deviation from unlogged natural forest at the microsite level. With the exception of one replicate (S‐C), simple trenching (S‐A and S‐B) was the treatment exerting the lowest incidence on soil multifunctional profile (Fig. 2A).


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)

Multifunctional comparison of soil samples according to their physicochemical (C, N, C:N ratio, pH, texture), trace gas exchanges (H2, CO, CO2) and abundance of bacteria (16S rRNA gene abundance; labelled as ‘Biomass’ in the plot) profiles. (A) UPGMA agglomerative clustering of soil samples according to a Euclidean distance matrix calculated with standardized variables. The grey circles denote the nodes delineating the four multifunctional classes significantly discriminated by SIMPROF permutation procedure (P < 0.05). 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). The scale bar represents the Euclidean distance in the dendrogram. (B) Principal component analysis showing the distribution of sampling sites in a reduced space defined by soil physicochemical properties, gaseous exchanges and abundance of bacteria. The colours used to present soil samples correspond to the clusters identified in the UPGMA (A). (C) Variables defining the distribution of soil samples along the first and the second axis are represented along with the equilibrium circle of descriptors showing the contribution of variables to the formation of the reduced space. The detection limit of the qPCR assay was utilized to estimate the abundance bacteria in sample M‐A for which the low yield of the DNA extraction procedure precluded qPCR and bacterial 16S rRNA gene profiling (see the Material and Methods section for more details).
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Related In: Results  -  Collection

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mbt212348-fig-0002: Multifunctional comparison of soil samples according to their physicochemical (C, N, C:N ratio, pH, texture), trace gas exchanges (H2, CO, CO2) and abundance of bacteria (16S rRNA gene abundance; labelled as ‘Biomass’ in the plot) profiles. (A) UPGMA agglomerative clustering of soil samples according to a Euclidean distance matrix calculated with standardized variables. The grey circles denote the nodes delineating the four multifunctional classes significantly discriminated by SIMPROF permutation procedure (P < 0.05). 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). The scale bar represents the Euclidean distance in the dendrogram. (B) Principal component analysis showing the distribution of sampling sites in a reduced space defined by soil physicochemical properties, gaseous exchanges and abundance of bacteria. The colours used to present soil samples correspond to the clusters identified in the UPGMA (A). (C) Variables defining the distribution of soil samples along the first and the second axis are represented along with the equilibrium circle of descriptors showing the contribution of variables to the formation of the reduced space. The detection limit of the qPCR assay was utilized to estimate the abundance bacteria in sample M‐A for which the low yield of the DNA extraction procedure precluded qPCR and bacterial 16S rRNA gene profiling (see the Material and Methods section for more details).
Mentions: Soil physicochemical properties, gaseous exchanges and bacteria abundance variables were utilized to define a multifunctional soil classification. Under this classification approach, the distribution of each variable was considered to compute a distance matrix measuring the association between soil samples (Fig. 2A). Four different multifunctional classes were identified in the clustering analysis. The level of disturbance characterizing each class was defined on the basis of their Euclidean distance from the unlogged natural forest plots. Firstly, the soil sample constituting class I (M‐B) represented the MSP treatment that resulted in the most intense disturbance of baseline ecological functions. Secondly, soil samples included in class II (S‐A, S‐B) belong to the category of MSP treatments that caused slight deviations from baseline soil ecological functions. Soil samples belonging to class III (N‐B, N‐A, N‐C) correspond to baseline of soil ecological functions. Finally, class IV (S‐C, I‐A, I‐C, I‐B, M‐A, M‐C, D‐A, D‐B and D‐C) encompass soils for which the MSP treatments caused important alteration of baseline ecological functions at the microsite level. The unlogged natural forest was the sole condition for which replicated composite samples exhibited treatment‐specific, conserved multifunctional profile. Taken together, this classification model indicates that soil multifunctional profile observed in inversion and mound excavations plots were those showing the strongest deviation from unlogged natural forest at the microsite level. With the exception of one replicate (S‐C), simple trenching (S‐A and S‐B) was the treatment exerting the lowest incidence on soil multifunctional profile (Fig. 2A).

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