Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A ...Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.
Deciphering ocean carbon in a changing world Moran, Mary Ann; Elizabeth B. Kujawinski; Aron Stubbins ...
Proceedings of the National Academy of Sciences - PNAS,
03/2016, Letnik:
113, Številka:
12
Journal Article
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Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO â reservoir. A vast number of compounds are present in ...DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO â in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
Groundwater constitutes a globally important source of freshwater for drinking water and other agricultural and industrial purposes, and is a prominent source of freshwater flowing into the coastal ...ocean. Therefore, understanding the chemical components of groundwater is relevant to both coastal and inland communities. We used electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to examine dissolved organic compounds in groundwater prior to and after passage through a sediment-filled column containing microorganisms. The data revealed that an unexpectedly high proportion of organic compounds contained nitrogen and sulfur, possibly due to transport of surface waters from septic systems and rain events. We matched 292 chemical features, based on measured mass:charge (
m/z) values, to compounds stored in the Kyoto Encyclopedia of Genes and Genomes (KEGG). A subset of these compounds (88) had only one structural isomer in KEGG, thus supporting tentative identification. Most identified elemental formulas were linked with metabolic pathways that produce polyketides or with secondary metabolites produced by plants. The presence of polyketides in groundwater is notable because of their anti-bacterial and anti-cancer properties. However, their relative abundance must be quantified with appropriate analyses to assess any implications for public health.
► ESI FT-ICR-MS was applied to DOM extracts from Lake Superior and its watershed. ► Chemical similarity was related to hydrological proximity and flow conditions. ► Lake Superior DOM was ...distinguished by lignin-like and reduced hydrocarbon formulae. ► Lake Superior DOM had a higher proportion of formulae containing nitrogen or sulfur. ► There was a conserved portion of formulae across the watershed’s DOM samples.
With the advent of ultrahigh resolution mass spectrometry (MS), recent studies have begun to resolve molecular relationships between terrestrial and aquatic dissolved organic matter (DOM) in rivers, estuaries, mangrove swamps and their receiving oceans and lakes. Here, we extend ultrahigh resolution MS techniques to Lake Superior, the largest freshwater lake in the world by area. Solid-phase extracted samples from the western arm of the lake and its watershed, including swamp, creek, river, lake–river confluence and offshore lake sites were compared using electrospray ionization (ESI), Fourier transform ion cyclotron resonance MS (FT-ICR-MS). Results were analyzed using cluster analysis and van Krevelen diagrams. Chemical similarity appears related to hydrological proximity, terrestrial impact and flow conditions. For example, higher and lower flow samples from the same stream differ from one another. Toivola Swamp, Lake Superior and the south shore river have diverse arrays of unique molecular formulae relative to the north shore river and stream sampled in the data set. The lake’s unique elemental formulae, relative to its watershed samples, are primarily in the lignin-like and reduced hydrocarbon regions of van Krevelen diagrams. The ESI-amenable lake DOM also has a higher proportion of formulae containing nitrogen or sulfur relative to the other samples. The degree of overlap among formulae within the data set is consistent with previous ESI FT-ICR-MS characterization of terrestrial, estuarine and marine OM. There appears to be a conserved portion of formulae across natural OM samples, perhaps because these compounds are intrinsically refractory or because they are commonly generated as products of natural reworking processes.
Marine dissolved organic matter (DOM) is one of the most heterogeneous and largest pools of reactive carbon on earth, rivaling in mass the carbon in atmospheric carbon dioxide. Nevertheless, the ...molecular-level composition of marine DOM has eluded detailed description, impeding inquiry into the specific mechanisms that add or remove compounds from the DOM pool. Here we describe the molecular-level composition of C
18-extracted DOM along an east–west transect of the North Atlantic Ocean. We examine the changes in DOM composition along this transect with ultrahigh resolution mass spectrometry and multivariate statistics. We use indicator species analysis (ISA) to identify possible source markers for photochemical degradation and heterotrophic bacterial metabolism. The inclusion of ISA in statistical evaluation of DOM mass spectral data allows investigators to determine the
m/z values associated with significant changes in DOM composition. With this technique, we observe indicator
m/z values in estuarine water that may represent components of terrestrially-derived chromophoric DOM subject to photochemical degradation. We also observe a unique set of
m/z values in surface seawater and show that many of these are present in pure cultures of the marine α-proteobacterium ‘‘
Candidatus Pelagibacter ubique” when grown in natural seawater. These findings indicate that a complex balance of abiotic and biotic processes controls the molecular composition of marine DOM to produce signatures that are characteristic of different environments.
Metabolomics is the study of small molecules, or ‘metabolites’, that are the end products of biological processes. While -omics technologies such as genomics, transcriptomics, and proteomics measure ...the metabolic potential of organisms, metabolomics provides detailed information on the organic compounds produced during metabolism and found within cells and in the environment. Improvements in analytical techniques have expanded our understanding of metabolomics and developments in computational tools have made metabolomics data accessible to a broad segment of the scientific community. Yet, metabolomics methods have only been applied to a limited number of projects in the marine environment. Here, we review analysis techniques for mass spectrometry data and summarize the current state of metabolomics databases. We then describe a boutique database developed in our laboratory for efficient data analysis and selection of mass spectral targets for metabolite identification. The code to implement the database is freely available on GitHub (https://github.com/joefutrelle/domdb). Data organization and analysis are critical, but often under-appreciated, components of metabolomics research. Future advances in environmental metabolomics will take advantage of continued development of new tools that facilitate analysis of large metabolomics datasets.
•We review analysis techniques for mass spectrometry data and existing metabolomics databases.•We describe a boutique database developed in our laboratory for data organization and analysis.•Future advances in environmental metabolomics will require new tools to analyze metabolomics data.
It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum
evolved specialized metabolisms for the oxidation of organic compounds that are ...resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent
hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.
The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.
Changes in sea ice in the Arctic will have ramifications on regional and global carbon cycling. Research to date has primarily focused on the regional impacts to biological activity and global ...impacts on atmospheric processes. The current project considers the molecular-level composition of organic carbon within sea ice compared to the organic matter in seawater. The project revealed that the composition of organic matter within sea ice was more variable than the composition of organic matter within the surface ocean. Furthermore, sea ice samples presented two distinct patterns in the composition of organic matter with a portion of the sea ice samples containing protein-like organic matter. Yet, the samples were collected in the early winter period when little biological activity is expected. Thus, one hypothesis is that physical processes acting during the formation of sea ice selectively transferred organic matter from seawater into sea ice. The present project expands our understanding of dissolved organic matter in sea ice and surface seawater and thereby increases our knowledge of carbon cycling in polar regions.
Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic ...Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades,
, and
, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
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