The Generalized Plant Allometry that Advances Metabolic Ecology Theory

Plant allometry is key for determining the role of forests in global carbon cycles, through the calculation of tree biomass using proxy measurements such as tree diameters or heights. Metabolic ecology theory (MET) considers the general principles that underpin allometry, but MET scaling relationships have been challenged on their lack of fit to empirical data and global applicability. We postulated that MET scaling is applicable only for plant tissues combining conductive and supportive functionality (tracheids), but as plants evolved tissues of specialized conductive functionality (vessels) their allometry progressed into more complex relationships. According to this principle, we deducted generalized MET (gMET) relationships with mechanistically deducted coefficients. Our gMET models proved to have exceptional empirical support against global datasets, achieving unbiased predictions across biomes worldwide. These results prove gMET models to be a crucial improvement to MET-based allometry, providing a universally applicable theoretical framework for worldwide estimations of forest carbon.

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

ABSTRACTReverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically-relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the thiamine biosynthesis and GAL pathways. As a result, optimal codon usage in thiamine biosynthesis genes is also associated with dairy ecological niches in Saccharomycetaceae, which may reflect competition with co-occurring microbes for extracellular thiamine. This work highlights the potential of codon optimization as a tool for gaining insights into the metabolic ecology of microbial eukaryotes. Doing so may be especially illuminating for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.

Height-diameter Relationships in Longleaf Pine and Four Swamp Tree Species

The scaling relationship between height and diameter is important for understanding the dynamic patterns of tree growth and estimating the accrual of tree biomass. Metabolic ecology predicts that tree growth follows a universal scaling invariant relative to the height-diameter relationship (i.e., no variation based on taxonomy or resource availability). Comparing field data for different tree species across a range of site conditions should be an informative test of that prediction. Our results indicate that the scaling exponents of height and diameter for longleaf pine (Pinus palustris Mill.) vary at the four locations across its natural range. As for swamp trees, the scaling exponents for red maple (Acer rubrum L.) and river birch (Betula nigra L.) were consistent with that predicted by metabolic ecology; however, those for water tupelo (Nyssa aquatica L.) and bald cypress (Taxodium distichum (L.) Rich) were not. Our study confirms that high plasticity and variation in allometric scaling of the tree height and diameter relationship may very well be the rule, rather than the exception.