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Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth’s subsurface and surface environments. 

Microbes and sunlight convert terrigenous dissolved organic matter (DOM) in surface waters to greenhouse gases. Prior studies show contrasting results about how biological and photochemical processes interact to contribute to the degradation of DOM. In this study, DOM leached from the organic layer of tundra soil was exposed to natural sunlight or kept in the dark, incubated in the dark with the natural microbial community, and analyzed for gene expression and DOM chemical composition. Microbial gene expression (metatranscriptomics) in light and dark treatments diverged substantially after 4 hours. Gene expression suggested that sunlight exposure of DOM initially stimulated microbial growth by (a) replacing the function of enzymes that degrade higher molecular weight DOM such as enzymes for aromatic carbon degradation, oxygenation, and decarboxylation, and (b) releasing low molecular weight compounds and inorganic nutrients from DOM. However, growth stimulation following sunlight exposure of DOM came at a cost. Sunlight depleted the pool of aromatic compounds that supported microbial growth in the dark treatment, ultimately causing slower growth in the light treatment over 5 days. These first measurements of microbial metatranscriptomic responses to photo-alteration of DOM provide a mechanistic explanation for how sunlight exposure of terrigenous DOM alters microbial processing and respiration of DOM. 

Abstract Most terrestrial allochthonous organic matter enters river networks through headwater streams during high flow events. In headwaters, allochthonous inputs are substantial and variable, but become less important in streams and rivers with larger watersheds. As allochthonous dissolved organic matter (DOM) moves downstream, the proportion of less aromatic organic matter with autochthonous characteristics increases. How environmental factors converge to control this transformation of DOM at a continental scale is less certain. We hypothesized that the amount of time water has spent travelling through surface waters of inland systems (streams, rivers, lakes, and reservoirs) is correlated to DOM composition. To test this hypothesis, we used established river network scaling relationships to predict relative river network flow‐weighted travel time (FWTT) of water for 60 stream and river sites across the contiguous United States (3090 discrete samples over 10 water years). We estimated lentic contribution to travel times with upstream in‐network lake and reservoir volume. DOM composition was quantified using ultraviolet and visible absorption and fluorescence spectroscopy. A combination of FWTT and lake and reservoir volume was the best overall predictor of DOM composition among models that also incorporated discharge, specific discharge, watershed area, and upstream channel length. DOM spectral slope ratio (R² = 0.77) and Freshness Index (R² = 0.78) increased and specific ultraviolet absorbance at 254 nm (R² = 0.68) and Humification Index (R² = 0.44) decreased across sites as a function of FWTT and upstream lake volume. This indicates autochthonous‐like DOM becomes continually more dominant in waters with greater FWTT. We assert that river FWTT can be used as a metric of the continuum of DOM composition from headwaters to rivers. The nature of the changes to DOM composition detected suggest this continuum is driven by a combination of photo‐oxidation, biological processes, hydrologically varying terrestrial subsidies, and aged groundwater inputs.