Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry

Tfaily, Malak M.; Chu, Rosalie K.; Toyoda, Jason; Tolić, Nikola; Robinson, Eric; Paša‐Tolić, Ljiljana; Hess, Nancy

doi:10.1016/j.aca.2017.03.031

Cited by 120 publications

(118 citation statements)

References 30 publications

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“…These metabolites were broadly categorized into eight groups: amino acids, acids, sugars, amines, polyols, choline, alcohols, and aromatic compounds. Sugars and acids were the most abundant metabolites and represented the highest concentration of total measured metabolites, with ~3,360 µM and ~1,010 µM in total per 50 mg of Sphagnum in 1 ml of DI H 2 O (extraction efficiency ~ 15%, Tfaily et al , ), respectively. Fructose was the most abundant measured metabolite present in Sphagnum (sugar; 2,490 µM), followed by glucose (sugar; 796 µM), malate (acid; 555 µM), and glycerol (polyol; 254 µM).…”

Section: Resultsmentioning

confidence: 96%

“…Van Krevelen diagrams provide a means to visualize and compare the average properties of organic compounds and assign compounds to the major biochemical classes (e.g., lipid‐, protein‐, lignin‐, carbohydrate‐, and condensed aromatic‐like). In this study, biochemical compound classes are reported as relative abundance values based on counts of C, H, and O for the following H:C and O:C ranges: lipids (0 < O:C ≤ 0.3 and 1.5 ≤ H:C ≤ 2.5), unsaturated hydrocarbons (0 ≤ O:C ≤ 0.125 and 0.8 ≤ H:C < 2.5), proteins (0.3 < O:C ≤ 0.55 and 1.5 ≤ H:C ≤ 2.3), amino sugars (0.55 < O:C ≤ 0.7 and 1.5 ≤ H:C ≤ 2.2), lignin (0.125 < O:C ≤ 0.65 and 0.8 ≤ H:C < 1.5), tannins (0.65 < O:C ≤ 1.1 and 0.8 ≤ H:C < 1.5), and condensed hydrocarbons (aromatics; 0 ≤ 200 O:C ≤ 0.95 and 0.2 ≤ H:C < 0.8; Tfaily et al, , ). It is important to note that FTICR‐MS by direct injection does not differentiate between isomers (i.e., compounds with same m/z, same molecular formula but different structure).…”

Section: Methodsmentioning

confidence: 99%

“…To ensure consistent formula assignment, we aligned all sample peak lists for the entire dataset to each other in order to facilitate consistent peak assignments and eliminate possible mass shifts that would impact formula assignment. We implemented the following rules to further ensure consistent formula assignment: (a) we consistently picked the Tfaily et al, 2015Tfaily et al, , 2017. It is important to note that FTICR-MS by direct injection does not differentiate between isomers (i.e., compounds with same m/z, same molecular formula but different structure).…”

Section: Organic Matter Metabolite Extractionmentioning

confidence: 99%

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Untargeted metabolomic profiling ofSphagnum fallaxreveals novel antimicrobial metabolites

et al. 2019

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Sphagnum mosses dominate peatlands by employing harsh ecosystem tactics to prevent vascular plant growth and microbial degradation of these large carbon stores. Knowledge about Sphagnum‐produced metabolites, their structure and their function, is important to better understand the mechanisms, underlying this carbon sequestration phenomenon in the face of climate variability. It is currently unclear which compounds are responsible for inhibition of organic matter decomposition and the mechanisms by which this inhibition occurs. Metabolite profiling of Sphagnum fallax was performed using two types of mass spectrometry (MS) systems and 1H nuclear magnetic resonance spectroscopy (1H NMR). Lipidome profiling was performed using LC‐MS/MS. A total of 655 metabolites, including one hundred fifty‐two lipids, were detected by NMR and LC‐MS/MS—329 of which were novel metabolites (31 unknown lipids). Sphagum fallax metabolite profile was composed mainly of acid‐like and flavonoid glycoside compounds, that could be acting as potent antimicrobial compounds, allowing Sphagnum to control its environment. Sphagnum fallax metabolite composition comparison against previously known antimicrobial plant metabolites confirmed this trend, with seventeen antimicrobial compounds discovered to be present in Sphagnum fallax, the majority of which were acids and glycosides. Biological activity of these compounds needs to be further tested to confirm antimicrobial qualities. Three fungal metabolites were identified providing insights into fungal colonization that may benefit Sphagnum. Characterizing the metabolite profile of Sphagnum fallax provided a baseline to understand the mechanisms in which Sphagnum fallax acts on its environment, its relation to carbon sequestration in peatlands, and provide key biomarkers to predict peatland C store changes (sequestration, emissions) as climate shifts.

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Section: Resultsmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

Section: Organic Matter Metabolite Extractionmentioning

confidence: 99%

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Untargeted metabolomic profiling ofSphagnum fallaxreveals novel antimicrobial metabolites

et al. 2019

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Section: Methodsmentioning

confidence: 99%

“…Samples were prepared according to Tfaily et al 2017. 46 Briefly, 1 mL of 18.2 MΩ Milli-Q water (EMD Millipore, Billerica, MA) was added to 300 mg bulk soil, vortexed for 20 sec and then put onto an Eppendorf Thermomixer at 1000 rpm and 20°C for 4 hours. Samples were then removed from the mixer and spun down before the supernatant was pulled off frozen and the final 1 mL chloroform was added and the samples were shaken overnight was described above.…”

Section: Methodsmentioning

confidence: 99%

Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils

Bhattacharyya

Campbell

Tfaily

et al. 2018

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37Oscillating redox conditions are the norm in tropical soils; driven by an ample supply of reductants, 38 high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. Yet 39 the net result of variable soil redox regimes on iron-organic matter (Fe-OM) associations in 40 tropical soils owing to changing climate is poorly understood. Using a 44-day redox incubation 41 experiment with humid tropical soils from Puerto Rico, we examined patterns of Fe and C 42 transformation under four redox regimes: static anoxic, flux 4-day (4d oxic, 4d anoxic), flux 8-day 43 (8d oxic , 4d anoxic) and static anoxic. Prolonged anoxia promoted reductive dissolution of Fe-44 oxides and an increase in short-range ordered (SRO) Fe oxides. Preferential dissolution of this 45 less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to 46 anoxic), and coincided with increased dissolved organic carbon, presumably due to acidification 47 or direct release of OM from dissolving Fe(III) mineral phases. Average nominal oxidation state 48 of water-soluble carbon was lowest under persistent anoxic conditions, suggesting more reduced 49 OC is microbially preserved under reducing conditions. Anoxic soil compounds had high H/C 50 values (similar to lignin-like metabolites) whereas oxic soil compounds had higher O/C values, 51 akin to tannin-and cellulose-like components. Cumulative respiration derived from native soil 52 organic carbon was highest in static oxic soils. These results highlight the volatility of mineral-53 OM interactions in tropical soils, and suggest that short-term impacts of shifting soil O2 availability 54 control exchanges of C between mineral-sorbed and aqueous pools, implying that the periodicity 55 of low-redox moments may control the fate of C in wet tropical soils. 56 57 58Wet tropical soils frequently alternate between fully oxygenated and anaerobic conditions, 60 making them biogeochemical 'hotspots' for redox reactions. [1][2][3][4][5][6] In the wet tropics, soils are often 61 dominated by iron (Fe) (and aluminum) rich clays and oxides that sorb organic carbon (C), but are 62 also susceptible to redox-induced mineral transformations. 6-10 The rapid Fe and C cycling typical 63 of wet tropical ecosystems is fueled by a characteristically dynamic redox environment driven by 64 high biological oxygen demand, high moisture (limiting O2 diffusion), warm temperatures and 65 abundant labile C. Unlike classically defined low-redox soils (e.g. wetlands) 11 where redox 66 zonation can be relatively static in time and space, redox oscillations in upland tropical forest soils 67 are spatially and temporally heterogeneous, likely occurring at the individual aggregate scale and 68 responding rapidly (hourly to daily) 6, 12, 13 to variations in rainfall and dissolved organic carbon 69 (DOC) inputs. 70 Iron minerals play a critical role in the C cycle of highly weathered tropical soils, 71 particularly where frequent cycles of reduction and oxidation fuel a large port...

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Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes

et al. 2017

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In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial‐aquatic interfaces are crucial to future climate predictions. Here we investigate the biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultrahigh‐resolution C characterization. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically bound OC. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in direct conflict with the “priming” concept—that inputs of water‐soluble and thermodynamically favorable terrestrial OC protect bound‐OC from oxidation. In both environments, the most thermodynamically favorable compounds appear to be preferentially oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular pool of OC but that common thermodynamic principles govern the oxidation of each pool (i.e., water‐soluble or physically bound). Finally, we propose a mechanistic conceptualization of OC oxidation along terrestrial‐aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.

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Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry

Cited by 120 publications

References 30 publications

Untargeted metabolomic profiling ofSphagnum fallaxreveals novel antimicrobial metabolites

Untargeted metabolomic profiling ofSphagnum fallaxreveals novel antimicrobial metabolites

Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils

Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes

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