Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater ...mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.
Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in ...nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ
C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF,
and
, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.
A vast number of organic compounds are present in soil organic matter (SOM) and play an important role in the terrestrial carbon cycle, facilitate interactions between organisms, and represent a sink ...for atmospheric CO2. The diversity of different SOM compounds and their molecular characteristics is a function of the organic source material and biogeochemical history. By understanding how SOM composition changes with sources and the processes by which it is biogeochemically altered in different terrestrial ecosystems, it may be possible to predict nutrient and carbon cycling, response to system perturbations, and impact of climate change will have on SOM composition. In this study, a sequential chemical extraction procedure was developed to reveal the diversity of organic matter (OM) in different ecosystems and was compared to the previously published protocol using parallel solvent extraction (PSE). We compared six extraction methods using three sample types, peat soil, spruce forest soil and river sediment, so as to select the best method for extracting a representative fraction of organic matter from soils and sediments from a wide range of ecosystems. We estimated the extraction yield of dissolved organic carbon (DOC) by total organic carbon analysis, and measured the composition of extracted OM using high resolution mass spectrometry. This study showed that OM composition depends primarily on soil and sediment characteristics. Two sequential extraction protocols, progressing from polar to non-polar solvents, were found to provide the highest number and diversity of organic compounds extracted from the soil and sediments. Water (H2O) is the first solvent used for both protocols followed by either co-extraction with methanol-chloroform (MeOH-CHCl3) mixture, or acetonitrile (ACN) and CHCl3 sequentially. The sequential extraction protocol developed in this study offers improved sensitivity, and requires less sample compared to the PSE workflow where a new sample is used for each solvent type. Furthermore, a comparison of SOM composition from the different sample types revealed that our sequential protocol allows for ecosystem comparisons based on the diversity of compounds present, which in turn could provide new insights about source and processing of organic compounds in different soil and sediment types.
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•ESI-FTICR-MS provides molecular characterization of soil organic molecules.•Sequential extraction increases the diversity of organic molecules detected.•Organic molecular diversity distinguishes soils from different ecosystems.
Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal ...organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics 'meta-metabolome ecology' and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.
Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. Using ...ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH4HCO3 from both the organic- and mineral-layer soils during incubation at both −2 and 8 °C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classes of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.
The hyporheic corridor (HC) encompasses the river-groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a ...novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology-biochemistry-microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW-RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.
Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the ...application of ultrahigh resolution mass spectrometry to profile the molecular composition of SOM and its degradation during a simulated warming experiment. A soil sample, collected near Barrow, Alaska, USA, was subjected to a 40-day incubation under anoxic conditions and analyzed before and after the incubation to determine changes of SOM composition. A CHO index based on molecular C, H, and O data was utilized to codify SOM components according to their observed degradation potentials. Compounds with a CHO index score between -1 and 0 in a water-soluble fraction (WSF) demonstrated high degradation potential, with a highest shift of CHO index occurred in the N-containing group of compounds, while similar stoichiometries in a base-soluble fraction (BSF) did not. Additionally, compared with the classical H:C vs O:C van Krevelen diagram, CHO index allowed for direct visualization of the distribution of heteroatoms such as N in the identified SOM compounds. We demonstrate that CHO index is useful not only in characterizing arctic SOM at the molecular level but also enabling quantitative description of SOM degradation, thereby facilitating incorporation of the high resolution MS datasets to future mechanistic models of SOM degradation and prediction of greenhouse gas emissions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing ...microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli, Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.
Abstract
Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root ...exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (
Bouteloua gracilis
Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.
Organic aerosol formation and transformation occurs within aqueous aerosol and cloud droplets, yet little is known about the composition of high molecular weight organic compounds in cloud water. ...Cloud water samples collected at Whiteface Mountain, New York, during August–September 2014 were analyzed by ultra-high-resolution mass spectrometry to investigate the molecular composition of dissolved organic carbon, with a focus on sulfur- and nitrogen-containing compounds. Organic molecular composition was evaluated in the context of cloud water inorganic ion concentrations, pH, and total organic carbon concentrations to gain insights into the sources and aqueous-phase processes of the observed high molecular weight organic compounds. Cloud water acidity was positively correlated with the average oxygen : carbon ratio of the organic constituents, suggesting the possibility for aqueous acid-catalyzed (prior to cloud droplet activation or during/after cloud droplet evaporation) and/or radical (within cloud droplets) oxidation processes. Many tracer compounds recently identified in laboratory studies of bulk aqueous-phase reactions were identified in the cloud water. Organosulfate compounds, with both biogenic and anthropogenic volatile organic compound precursors, were detected for cloud water samples influenced by air masses that had traveled over forested and populated areas. Oxidation products of long-chain (C10−12) alkane precursors were detected during urban influence. Influence of Canadian wildfires resulted in increased numbers of identified sulfur-containing compounds and oligomeric species, including those formed through aqueous-phase reactions involving methylglyoxal. Light-absorbing aqueous-phase products of syringol and guaiacol oxidation were observed in the wildfire-influenced samples, and dinitroaromatic compounds were observed in all cloud water samples (wildfire, biogenic, and urban-influenced). Overall, the cloud water molecular composition depended on air mass source influence and reflected aqueous-phase reactions involving biogenic, urban, and biomass burning precursors.
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