Does soil pyrogenic carbon determine plant functional traits in Amazon Basin forests?

Amazon forests are fire-sensitive ecosystems and consequently fires affect forest structure and composition. For instance, the legacy of past fire regimes may persist through some species and traits that are found due to past fires. In this study, we tested for relationships between functional traits that are classically presented as the main components of plant ecological strategies and environmental filters related to climate and historical fires among permanent mature forest plots across the range of local and regional environmental gradients that occur in Amazonia. We used percentage surface soil pyrogenic carbon (PyC), a recalcitrant form of carbon that can persist for millennia in soils, as a novel indicator of historical fire in old-growth forests. Five out of the nine functional traits evaluated across all 378 species were correlated with some environmental variables. Although there is more PyC in Amazonian soils than previously reported, the percentage soil PyC indicated no detectable legacy effect of past fires on contemporary functional composition. More species with dry diaspores were found in drier and hotter environments. We also found higher wood density in trees from higher temperature sites. If Amazon forest past burnings were local and without distinguishable attributes of a widespread fire regime, then impacts on biodiversity would have been small and heterogeneous. Alternatively, sufficient time may have passed since the last fire to allow for species replacement. Regardless, as we failed to detect any impact of past fire on present forest functional composition, if our plots are representative then it suggests that mature Amazon forests lack a compositional legacy of past fire.     

Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases

Eukaryotes and archaea both possess multiple genes coding for family B DNA polymerases. In animals and fungi, three family B DNA polymerases, alpha, delta, and epsilon, are responsible for replication of nuclear DNA. We used a PCR-based approach to amplify and sequence phylogenetically conserved regions of these three DNA polymerases from Giardia intestinalis and Trichomonas vaginalis, representatives of early-diverging eukaryotic lineages. Phylogenetic analysis of eukaryotic and archaeal paralogs suggests that the gene duplications that gave rise to the three replicative paralogs occurred before the divergence of the earliest eukaryotic lineages, and that all eukaryotes are likely to possess these paralogs. One eukaryotic paralog, epsilon, consistently branches within archaeal sequences to the exclusion of other eukaryotic paralogs, suggesting that an epsilon-like family B DNA polymerase was ancestral to both archaea and eukaryotes. Because crenarchaeote and euryarchaeote paralogs do not form monophyletic groups in phylogenetic analysis, it is possible that archaeal family B paralogs themselves evolved by a series of gene duplications independent of the gene duplications that gave rise to eukaryotic paralogs.      

Influence of habitat,litter type,and soil invertebrates on leaf-litter decomposition in a fragmented Amazonian landscape

Amazonian forest fragments and second-growth forests often differ substantially from undisturbed forests in their microclimate, plant-species composition, and soil fauna. To determine if these changes could affect litter decomposition, we quantified the mass loss of two contrasting leaf-litter mixtures, in the presence or absence of soil macroinvertebrates, and in three forest habitats. Leaf-litter decomposition rates in second-growth forests (>10 years old) and in fragment edges (<100 m from the edge) did not differ from that in the forest interior (>250 m from the edges of primary forests). In all three habitats, experimental exclusion of soil invertebrates resulted in slower decomposition rates. Faunal-exclosure effects were stronger for litter of the primary forest, composed mostly of leaves of old-growth trees, than for litter of second-growth forests, which was dominated by leaves of successional species. The latter had a significantly lower initial concentration of N, higher C:N and lignin:N ratios, and decomposed at a slower rate than did litter from forest interiors. Our results indicate that land-cover changes in Amazonia affect decomposition mainly through changes in plant species composition, which in turn affect litter quality. Similar effects may occur on fragment edges, particularly on very disturbed edges, where successional trees become dominant. The drier microclimatic conditions in fragment edges and second-growth forests (>10 years old) did not appear to inhibit decomposition. Finally, although soil invertebrates play a key role in leaf-litter decomposition, we found no evidence that differences in the abundance, species richness, or species composition of invertebrates between disturbed and undisturbed forests significantly altered decomposition rates.     

Widespread and ancient distribution of a noncanonical genetic code in diplomonads

Recently, a group of diplomonads has been found to use a genetic code in which TAA and TAG encode glutamine rather than termination. To survey the distribution of this characteristic in diplomonads, we sought to identify TAA and TAG codons at positions where glutamine is expected in genes for alpha-tubulin, elongation factor-1 alpha, and the gamma subunit of eukaryotic translation initiation factor-2. These sequences show that the variant genetic code is utilized by almost all diplomonads, with the genus Giardia alone using the universal genetic code. Comparative phylogenetic analysis reveals that the switch to this genetic code took place very early in the evolution of diplomonads and was likely a single event. Termination signals and downstream untranslated regions were also cloned from three Hexamita genes. In all three of these genes, the predicted TGA termination codon was found at the expected position. Interestingly, the untranslated regions of these genes are high in AT. This is incongruent with the coding regions, which are comparatively GC-rich.