Multivariate analyses in soil microbial ecology: a new paradigm

Thioulouse, Jean; Prin, Yves; Duponnois, Robin

doi:10.1007/s10651-012-0198-z

Cited by 21 publications

(19 citation statements)

References 47 publications

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“…The GLM is based on a flexible generalization of ordinary linear models that allows for response variables to follow other distributions than the normal distribution [28,29]. Poisson distributions were used on species present in 5 or more samples to avoid the issue of zero-inflated Poisson regression.…”

Section: General Linear Modelmentioning

confidence: 99%

Influence of regions, land uses and soil properties on termite and ant communities in agricultural landscapes of the Colombian Llanos

Sanabria

Dubs

Lavelle

et al. 2016

European Journal of Soil Biology

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Influence of regions, land uses and soil properties on termite and ant communities in agricultural landscapes of the Colombian Llanos. European Journal of Soil Biology, Elsevier, 2016, 74, pp.81-92 AbstractAnts and termites, as soil engineers, provide many ecosystem services that can be important for the sustainability of agriculture. The aim of this study was to evaluate the impact of land use on ant and termite communities in Colombian savanna landscapes, and to assess whether this impact is associated with the modification of soil physical and chemical properties. Ants and termites were sampled in five different agricultural and semi-natural systems across three regions of the 3 eastern Colombian Llanos: 1) annual crops (maize, soy and rice), 2) rubber plantations, 3) oil palm plantations, 4) improved pastures and 5) semi-natural savannas. A total of 91 ant and 16 termite species were collected. Multivariate analysis revealed that termite communities significantly differed among land uses, but not between regions. Ant communities differed between regions and land uses. Based on between group analyses of termite communities, three groups of land use can be distinguished: one formed by semi-natural savannas and improved pastures, the second by oil palm plantations and annual crops and the third by rubber plantations.General linear models applied separately to each species found 19 significant associations of soil physical or chemical properties, land uses or regions with 15 ant species and 14 significant associations with 6 termite species. Taken together, there is a strong association between land use and ant or termite communities and this influence is likely due to changes in ant and termite habitats resulting from agricultural practices such as tillage, fertilization, and lime addition. These results suggest that annual crops are the most detrimental land use for termites and ants, because their communities are highly sensitive to vegetation cover and agricultural practices such as tillage. Maintaining a high diversity of soil engineers and the ecosystem services they provide likely depends on the maintenance of natural ecosystems in the landscape and the adoption of practices that reduce impacts on soil ecosystem engineers when native ecosystems have been transformed into agricultural systems.

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Section: General Linear Modelmentioning

confidence: 99%

Influence of regions, land uses and soil properties on termite and ant communities in agricultural landscapes of the Colombian Llanos

Sanabria

Dubs

Lavelle

et al. 2016

European Journal of Soil Biology

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“…Data analysis proceeded in three steps: (i) the dudi.pca function was employed to perform a principal component analysis of a data frame, (ii) the s.corcircle function was used for plotting the preycategories axes and (iii) the s.class function was used to test differences in the projection of the feeding with ellipses and gravity centres grouped by species. For each month, in order to explore the statistical significance of the between group analysis (here species), a permutation test (Monte Carlo test) was used (Thioulouse et al, 2012). Statistical analyses and graphical outputs were performed using R 3.2.0 (R Core Team, 2012) utilizing the 'ade4' package (see Thioulouse et al, 1997).…”

Section: Statistical Analysesmentioning

confidence: 99%

Food resource partitioning between stream-dwelling Arctic charr Salvelinus alpinus (L.), Atlantic salmon Salmo salar L. and alpine bullhead Cottus poecilopus Heckel, 1836: an example of water column segregation

2015

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“…The use of multivariate analyses is supplanting 'simple' descriptive analyses across ecology (see James &McCulloch, 1990 andØkland, 2007 for comment) and has become common in microbial ecology, where complex, multidimensional data sets abound (e.g. Ramette, 2007;Bertics & Ziebis, 2009;Frossard et al, 2012;Thioulouse et al, 2012;Hartmann et al, 2013;Rivers et al, 2013). Indeed, numerous software tools used by microbial ecologists implement multivariate analysis techniques and have been recommended as standard components of, for example, microbiome analysis (Kuczynski et al, 2012) and environmental studies (e.g.…”

Section: Introductionmentioning

confidence: 99%

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

Buttigieg

Ramette

2014

FEMS Microbiology Ecology

310

198

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The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community.

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Multivariate analyses in soil microbial ecology: a new paradigm

Cited by 21 publications

References 47 publications

Influence of regions, land uses and soil properties on termite and ant communities in agricultural landscapes of the Colombian Llanos

Influence of regions, land uses and soil properties on termite and ant communities in agricultural landscapes of the Colombian Llanos

Food resource partitioning between stream-dwelling Arctic charr Salvelinus alpinus (L.), Atlantic salmon Salmo salar L. and alpine bullhead Cottus poecilopus Heckel, 1836: an example of water column segregation

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

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