Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are interlinked remains poorly characterized in fresh waters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5 times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5 to 2.7 times, when all of the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.

High‐resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive‐ion and negative‐ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified ~1000 common ions in both negative‐ and positive‐ion modes over a wide range of m/z values and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance‐weighted average indices (H/C, O/C, aromaticity, and m/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments.

Dissolved organic matter (DOM) in the oceans constitutes a major carbon pool involved in global biogeochemical cycles. More than 96% of the marine DOM resists microbial degradation for thousands of years. The composition of this refractory DOM (RDOM) exhibits a molecular signature ubiquitously detected in the deep oceans. Surprisingly efficient microbial transformation of labile into stable forms of DOM has been shown previously, implying that microorganisms apparently produce far more RDOM than needed to sustain the global pool. Here we show, by assessing the microbial formation and transformation of DOM in unprecedented molecular detail for 3 years, that most of the microbial DOM is different from RDOM in the ocean. Only <0.4% of the net community production is channelled into a form of DOM that is undistinguishable from oceanic RDOM. Our study provides a molecular background for global models on the production, turnover and accumulation of marine DOM.

Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10 000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined ‘species’, reflecting the functional diversity of microorganisms at high taxonomic resolution.

Estuaries as connectors of freshwater and marine aquatic systems are hotspots of biogeochemical element cycling. In one of the best studied temperate estuaries, the Delaware Estuary (USA), we investigated the variability of dissolved organic matter (DOM) over five sampling cruises along the salinity gradient in August and November of 3 consecutive years. Dissolved organic carbon (DOC) concentrations were more variable in the upper reaches of the estuary (245±49 µmol L-1) than at the mouth of the estuary (129±14 µmol L-1). Bulk DOC decreased conservatively along the transect in November but was non-conservative with increased DOC concentrations mid-estuary in August. Detailed analysis of the solid-phase extractable DOM pool via ultrahigh resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) revealed compositional differences at the molecular level that were not reflected in changes in concentration. Besides the mixing of terrestrial and marine endmember signatures, river discharge levels and biological activity were found to impact DOM molecular composition. DOM composition changed less between August and November than along the salinity gradient. Relative contributions of presumed photolabile DOM compounds did not reveal non-conservative behavior indicative of photochemical processing; suggesting that on the timescales of estuarine mixing photochemical removal of molecules plays a minor role in the turbid Delaware Bay. Overall, a large portion of molecular formulae overlapped between sampling campaigns and persisted during estuarine passage. Extending the analysis to the structural level via the fragmentation of molecular masses in the FT-ICR-MS cell, we found that the relative abundance of isomers along the salinity gradient did not change, indicating a high structural similarity of aquatic DOM independent of the origin. These results point towards a recalcitrant character of the DOM supplied by the Delaware River. We demonstrate that in addition to bulk DOC quantification, detailed information on molecular composition is essential for constraining sources of DOM and to identify the processes that impact estuarine DOM, thereby controlling amount and composition of DOM eventually discharged to the ocean through estuaries.