One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation-more so than for any other class of sites.

Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the biosphere. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also affect estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SADs) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33% of the total bacterial DNA pool but exceeded 80% in some samples. Despite its abundance, relic DNA had a minimal effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Our findings are consistent with the expectation that relic DNA from different taxa degrades at a constant and equal rate, suggesting that it may not fundamentally alter estimates of microbial diversity.

Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource-diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.