TreeDyn: towards dynamic graphics and annotations for analyses of trees

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions

Restriction of nodulation by the broad host range Rhizobium tropici strain CIAT899 in wild accessions of Phaseolus vulgaris L.

Common bean (Phaseolus vulgaris L.) is nodulated by a heterogeneous group of Rhizobium strains. In a search for host plant restriction of nodulation by some of these strains, 50 wild and cultivated bean accessions were evaluated for the length of time taken to form effective nodules with three diverse bean strains. As bean genotypes vary substantially for this character, preference or restriction was defined as a relative parameter between the three Rhizobium strains for a given bean genotype. Many of the bean genotypes evaluated showed no preference for particular strains of Rhizobium though Rhizobium strain CIAT8002 was often slowest to nodulate. Amongst the wild and landrace bean accessions, there was a tendency for materials of Mesoamerican origin to form active nodules more rapidly with CIAT632 (a Rhizobium leguminosarum bv. phaseoli strain isolated from Guatemala) than with CIAT899 (a broad host-range, R. tropici from Colombia). In contrast, in those cases in which some preference was observed, wild and landrace bean genotypes from Peru and Argentina (Andean origin) nodulated more rapidly with Rhizobium strain CIAT899. There were exceptions to this pattern among bred lines. Three wild bean accessions: G10002 from Mexico, G23418 from Costa Rica and G21117 from Colombia showed strong resistance to nodulation with CIAT899. Formation of effective nodules took more than 10 d longer with CIAT899 than with CIAT632. This strain preference was not altered by changing the time of inoculation between 0 and 8 d after sowing. Within an accession, plant to plant variation was observed in the time taken to nodulate with a given strain of Rhizobium. However this variation persisted in the progenies of contrasting individual plants of G21117