Simultaneous analysis of a sequence of paired ecological tables: A comparison of several methods

A pair of ecological tables is made of one table containing environmental variables (in columns) and another table containing species data (in columns). The rows of these two tables are identical and correspond to the sites where environmental variables and species data have been measured. Such data are used to analyze the relationships between species and their environment. If sampling is repeated over time for both tables, one obtains a sequence of pairs of ecological tables. Analyzing this type of data is a way to assess changes in species-environment relationships, which can be important for conservation Ecology or for global change studies. We present a new data analysis method adapted to the study of this type of data, and we compare it with two other methods on the same data set. All three methods are implemented in the ade4 package for the R environment.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS372 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Interactive Multivariate Data Analysis in R with the ade4 and ade4TkGUI Packages

ade4 is a multivariate data analysis package for the R statistical environment, and ade4TkGUI is a Tcl/Tk graphical user interface for the most essential methods of ade4. Both packages are available on CRAN. An overview of ade4TkGUI is presented, and the pros and cons of this approach are discussed. We conclude that command line interfaces (CLI) and graphical user interfaces (GUI) are complementary. ade4TkGUI can be valuable for biologists and particularly for ecologists who are often occasional users of R. It can spare them having to acquire an in-depth knowledge of R, and it can help first time users in a first approach.

Traitements nématicides et peuplement de nématodes parasites de la canne à sucre au Burkina Faso : 1. Repousses

International audienceNematicides and nematode community parasitic on sugarcane in Burkina Faso. 1. Ratoon cane Triadic analysis of three ways tables provides a means for studying the effect of nematicide treatments applied on sugarcane ratoons upon nematodes populations dynamics, by taking into account the between-plots variability of nematodes numbers. Only fumigation applied before planting has markedly reduced the size of the community. The treatments applied in ratoons next years has only a moderate effect upon nematode multiplication. For al! the treatments that we have compared, the size of the community tends to increase from ratoon to ratoon. Oxamyl, carbofuran and aldicarb, employed in ratoon, modify the balance between endoparasitic populations; their application is followed by the formation of a community dominated by Meloidogyne and Pratylenchus at the end of the crop. However, on the control, after the second ratoon the populations of Paratylenchus, Hoplo/aimus and Heterodera become more important than the populations of Meloidogyne and Pratylenchus. Helicotylenchus is more influenced by seasonal fluctuations than by treatments.L'analyse triadique de tableaux multiples a permis d'extraire les contraintes imposées à la dynamique des populations de nématodes par l'application de traitements nématicides sur des repousses de canne à sucre, sans éliminer la variabilité interparcellaire. Seule la fumigation effectuée avant la plantation a provoqué une baisse importante du volume du peuplement. Les traitements appliqués les années suivantes en repousse n'affectent que modérément la multiplication des nématodes. Dans toutes les séquences de traitements comparées, le volume du peuplement a tendance à s'accroître au fil des repousses. Oxamyl, carbofuran et aldicarbe, employés en repousse, modifient l'équilibre entre les populations d'endoparasites; ils conduisent à la constitution d'un peuplement dominé par Meloidogyne et Pratylenchus en fin de cycle. Par contre sur le témoin, à partir de la seconde repousse, les populations de Paratylenchus, Hoplolaimus et Heterodera deviennent plus importantes que celles de Meloidogyne et Pratylenchus. Helicotylenchus est plus affecté par les fluctuations saisonnières que par les traitements

A new process to promote the use of controlled mycorrhization practice in forest nurseries

The aims of this study were to test a new mycorrhizal inoculation process using a “catalyser” of the mycorrhizal establishment (termite mounds of Macrotermes subhyalinus) to minimize the requested volume of fungal inoculum added to the cultural substrate. The effects of the termite mound were explored on mycorrhiza formation between an Australian Acacia, Acacia holosericea and an ectomycorrhizal fungus or an arbuscular mycorrhizal fungus using a two-step cultural system. The first step of this cultural practice was the inoculation of A. holosericea seedlings in small soil volumes (5 L plastic containers planted with 100 pre-germinated seeds) whereas the second one allowed the development of these mycorrhized plants in larger soil volumes (1 L pots planted with one seedling). Termite mound amendment significantly enhanced the mycorrhizal formation from both types of fungal isolates. This stimulating effect could probably be attributed to the introduction via the termite mound of a bacterial group (that is, fluorescent pseudomonads) that could act as Mycorrhiza Helper Bacteria (MHB). Since it is possible to reduce the requested fungal inoculum in controlled mycorrhization practice using M. subhyalinus mound powders, this biotechnological process could be useful in re-afforestation of tropical regions by lowering the requested fungal inoculum quantities and reducing the financial costs of controlled mycorrhization in forest nurseries

Ectomycorrhizal-Dominated Boreal and Tropical Forests Have Distinct Fungal Communities, but Analogous Spatial Patterns across Soil Horizons

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0–20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling