publications

2026

1. aqualog2nc: Conversion of Origin Pro project files (OPJ) and workbook files (OGW) containing absorbance and fluorescence measurements to ACDD- and CF- compliant NetCDF files

   Urban Wünsch

   Aug 2026

   Abs DOI 0 citations

   Overview aqualog2nc reads Horiba AquaLog "3D Acquisition[EEM 3D CCD + Absorbance]" measurements straight out of Origin Pro’s .opj/.ogw project files and writes every sample it finds into a single NetCDF file. Give it one file or a whole folder; every sample from the file or folder ends up in the same output. Two passes happen internally: first every sample in the input is read into memory (its excitation/emission axes, its raw EEM/absorbance data, and some instrument settings pulled from the sample’s own Note sheet). Then samples are grouped by whether they share the exact same measurement configuration before anything is written. Blanks (no real sample data) and incomplete/aborted samples are detected and skipped automatically. The file’s "history" attribute records a full, timestamped audit trail of the run - every file read, every sample accepted, every sample skipped (with a reason), when each measurement itself actually completed, and a final summary - check there first if a sample you expected to see is missing. Only the raw, unprocessed instrument output is exported. Meaning no spectral correction (or other pre-processing) has happned. What you get is raw CCD/diode counts. You still need to do your own processing (dark subtraction, applying XCorrect/MCorrect, blank subtraction, inner-filter-effect correction, Raman-unit calibration, scatter removal, etc.) to turn this raw data into fully corrected absorbance spectra and fluorescence EEM fingerprints for your samples. As of this writing, the drEEM toolbox can do this processing. The output file also carries standard ACDD/CF discovery metadata (title, summary, keywords, instrument, Conventions, creation/processing dates, the time span the measurements cover, and a version tag for the aqualog2nc release that produced it) - useful if you’re archiving the file somewhere that indexes on that kind of metadata. Structure of the produced NetCDF file Samples that share the exact same excitation axis, emission axis, XCorrect, MCorrect, park wavelength, CCD gain factor, CCD pixel binning, and CCD gain/ADC settings are grouped together, since it would be wasteful to repeat identical axes/corrections for every single sample. Where all of this ends up depends on how many distinct measurement configurations the input actually contains: If every sample in the input shares one configuration (the common case for a single measurement campaign), there are no groups at all - everything sits directly at the root of the NetCDF file. If the input spans more than one configuration (e.g. you pointed the tool at a folder covering more than one instrument setup), each configuration gets its own group, named "measurement_type_1", "measurement_type_2", etc. (numbered, zero-padded, largest group first). Each group is a self-contained copy of the structure below. Either way, the structure inside root (or inside each group) is the same: Dimensions: data_identifier_i - one per sample in this bucket excitation, emission - the shared wavelength axes for every sample in this bucket Variables indexed by (data_identifier_i, excitation, emission): S1Sample - raw, entirely uncorrected fluorescence observations resulting from the excitation of the sample S1Blank - raw, entirely uncorrected fluorescence observations resulting from the excitation of the blank Variables indexed by (data_identifier_i, excitation): R1_Sample, R1_Blank - intensity of the reference diode at every excitation wavelength, during the sample/blank measurement AbsI1_Sample, AbsI1_Blank - raw, entirely uncorrected diode intensity after the attenuation of light by the sample/blank Variables indexed by (data_identifier_i, emission): S1Dark_Sample, S1Dark_Blank - CCD detector signal under dark conditions immediately prior to the sample/blank measurement All of the above are raw instrument output - you still need to apply your own corrections (see "WHAT THE TOOL DOES" above) to get a corrected EEM or absorbance spectrum out of them. Variables indexed by (data_identifier_i) only - one value per sample: data_identifier_i - the actual coordinate variable for this dimension: a plain, monotonically increasing integer (1, 2, 3, ...) with no other meaning, present because some strict CF compliance checkers require a dimension’s coordinate variable to hold monotonic values, which the human-readable identifier below can’t guarantee. data_identifier - the sample’s own identifier, exactly as it appears in Origin’s workbook browser (see "Sample identity" below). Not guaranteed unique - two samples can legitimately share one - so treat data_identifier_i as the reliable way to index a specific sample, and data_identifier as the human-readable label for it. R1dark_Sample, R1dark_Blank - intensity of the reference diode under dark conditions, immediately prior to the sample/blank measurement AbsI1dark_Sample, AbsI1dark_Blank - intensity of the absorbance diode under dark conditions, immediately prior to the sample/blank measurement integration_time - integration time used for the measurement park_wavelength_nm - fixed centering value of the emission detector ccd_gain_factor - detector gain factor ccd_xbin - pixel binning of the emission detector ccd_adc_readout - gain setting 1; ccd_gain - gain setting 2 workbook_name - sample identifier as retrieved from the workbook property; workbook_short_name - the short-identifier equivalent source_opj_file - the file from which the measurement was extracted experiment_file - the XML file from which the measurement was orchestrated creation_time - date/time the measurement finished; modification_time - date/time the data processing finished Variables indexed by their own axis only (shared, not per-sample): excitation, emission - the wavelength axes themselves (coordinate variables) XCorrect (excitation) - instrument-specific excitation correction factors for multiplication of signal MCorrect (emission) - instrument-specific emission correction factors for multiplication of signal A missing value anywhere (e.g. a report-derived setting the tool couldn’t find for a particular sample) is written as -9999 (or "-9999" for text fields), with a "missing_value" attribute declared on the variable per CF conventions - never silently left as some other placeholder. Every variable carries CF/ACDD-style attributes (standard_name, long_name, coverage_content_type, units, coordinates where applicable). The file’s global "history" attribute is a full, timestamped audit trail of the run that produced it: the exact command invoked, every input file read, every sample accepted or skipped (with a reason and which .opj file it came from), when each accepted sample’s measurement actually finished, how the grouping decision above was made, and a final summary - all entries sorted chronologically, so a sample’s own measurement time appears ahead of anything this run itself did. Check it first if a sample you expected to see is missing, or if you want a record of exactly what a given export run did. data_identifier comes from the sample’s own workbook name/label in Origin (exactly what you’d see in Origin’s own Project Explorer, or what a LongName property lookup would give you) - not from anything inside the compressed Note sheet, and not cross-checked against it either. Whatever the workbook is currently named is trusted as-is, including a rename made after the fact. Because of this, data_identifier is not guaranteed unique: two samples can legitimately share one (e.g. a genuine repeat measurement, or an operator reusing the same identifier by mistake) - they’re told apart by their position along the data_identifier_i dimension, not by the string itself. One exception is flagged automatically: if the same data_identifier turns up in two different source .opj files - which Origin itself has no way to catch, since it only ever sees one project at a time - every occurrence after the first file that used it gets "_duplicate" appended. This is an informational flag for findability, not a correctness gate; the sample’s data is exported normally either way.

2. Tips and Tricks for Organizing a Summer School—A Case Study Based on the “Nexus of Organic Matter Analytical Developments” School

   Alexander J Craig, Alina Mostovaya, Juliana D’Andrilli, and 12 more authors

   Limnology and Oceanography Bulletin, Apr 2026

   Abs DOI 0 citations

   In June 2025 we organized and ran the first “Nexus of Organic Matter Analytical Developments” (NOMAD) Summer School at the Tjärnö Marine Laboratory in Sweden. In this article, we describe its development and implementation, with the aim of offering practical insights into the planning process, a generalizable framework for future summer schools, and key recommendations for organizers. We describe how we conceptualized the summer school and justify why it was needed, and recount our processes to acquire funding, recruit teachers, advertise the program, and select students. Additionally, we discuss how we designed the educational and social program to strike a balance between formal and informal educational and social content. Finally, we include comments directly from students to provide useful context and counterpoints from participants at such events.

3. An ultraviolet–visible spectroscopy system for studying real‐time pressure effects on enzyme activity

   Maria Papadimitraki, Urban Wünsch, John Paul Balmonte, and 4 more authors

   Limnology and Oceanography: Methods, Jan 2026

   Abs DOI 0 citations

   Investigations of hydrostatic pressure effects on microbial enzymatic processing are challenging but critical for understanding element cycling in the world’s oceans. In this study, we developed and tested a stainless-steel pressure cell capable of withstanding up to 110 MPa of hydrostatic pressure (equivalent to 11,000 m depth), featuring three sapphire windows that enable real-time measurements of spectral absorption and fluorescence. The temperature-controlled system (5–50 C) can be incorporated in standard laboratory spectrofluorophotometers. The hydrostatic pressure of the 2.6 mL sample is regulated using a manually controlled spindle pump. The system was tested with fluorometric enzyme assays and used to evaluate the activity of chitinase enzymes produced by piezophilic and piezosensitive marine bacteria at a constant temperature of 10 C. Experiments on enzymes from three bacterial strains revealed distinct and reproducible differences in pressure responses. This compact system enables precise monitoring of pressure-sensitive activity of microbial communities and extracellular enzymes and thus provides an avenue for detailed investigations on the importance of hydrostatic pressure in regulating deep-sea biogeochemical processing.

4. Hydrostatic pressure induces strong leakage of dissolved organic matter from “marine snow” particles

   Peter Stief, Jutta Niggemann, Margot Bligh, and 5 more authors

   Science Advances, Feb 2026

   DOI 5 citations
5. Seasonal Characterization of Mercury and Organic Matter From the Contaminated Penobscot River to the Gulf of Maine

   Sophia K. Smith, Robert P. Mason, Vivien F. Taylor, and 2 more authors

   Journal of Geophysical Research: Biogeosciences, Jan 2026

   Abs DOI 0 citations

   Mercury (Hg), in the form of methylmercury (MeHg), is a neurotoxin that bioaccumulates in marine organisms and biomagnifies up the food chain. Understanding its behavior in coastal ecosystems is important, especially in fishing grounds such as the Gulf of Maine (GoM). Elevated inputs of terrestrial organic matter (OM) have been observed in the GoM, driven by increased watershed runoff from climate and land use changes. OM is an important vector for Hg transport in rivers, and OM character and concentration can influence the methylation and bioavailability of MeHg. To evaluate how increased watershed inputs would impact the GoM, the relationship between MeHg, Hg, OM quality and quantity, and other water parameters was assessed between April 2023–2024 during four cruises in the GoM and a major tributary, the historically Hgcontaminated Penobscot River, as well as during two trips further upstream. OM quality was evaluated via fluorescence spectrophotometry and a six‐component parallel factor analysis (PARAFAC) model identified two marine and four terrestrial OM components. Terrestrial OM proxies were strong predictors of, and positively correlated with, MeHg in the Penobscot River/Estuary, suggesting that co‐transport of MeHg and OM outweighs terrestrial OM’s attenuation of in situ methylation in the water column. We concluded however that the Penobscot River was not an important source of Hg to the GoM. Rather, a seasonally consistent hotspot of MeHg at depth in Jordan Basin was identified, correlating with elevated apparent oxygen utilization, nitrate, and other proxies for OM degradation suggesting its formation in situ in the deeper waters.

2025

1. Fluorescence as a tracer of the susceptibility of dissolved organic matter to photodegradation in the Arctic Ocean

   Urban J. Wünsch, Rafael Gonçalves‐Araujo, Mats A. Granskog, and 3 more authors

   Limnology and Oceanography, Jun 2025

   Abs DOI 6 citations

   The Arctic Ocean exports a large amount of terrestrial dissolved organic matter (DOM) to the Nordic seas. With climate change, the supply of terrestrial DOM from the Arctic Ocean will increase while less sea ice might lead to an increased loss of terrestrial DOM due to photodegradation. Here, we aimed to predict DOM photosensitivity based on fluorescence properties across the Eurasian Arctic. Exposures of seawater samples equaling approximately three d of surface irradiance at 85 N (above sea ice) were simulated. On average, 51% of fluorescence and 29% of DOM absorbance was lost while no significant photomineralization was observed. A N-way partial least squares model was trained to predict the average loss of DOM fluorescence relative to the start value (“photosensitivity index”) from the unexposed fluorescence landscapes. The prediction root mean squared error equaled 7.8% of the average predicted value. We applied the model to \textgreater 1500 samples spanning from the Lena River plume, across central Arctic, through Fram Strait, to Denmark Strait. For terrestrial DOM in polar water, the photosensitivity index notably decreased on the Siberian and East Greenland shelf, whereas local, distinct decreases in photosensitivity index were confined to the summer mixed layer in the Central Arctic Ocean. The qualitative photosensitivity index can indicate the occurrence and extent of photodegradation and could be used to monitor the effects of sea ice retreat and thinning in the Arctic Ocean.

2. Lena River biogeochemistry captured by a 4.5-year high-frequency sampling program

   Bennet Juhls, Anne Morgenstern, Jens Hölemann, and 24 more authors

   Earth System Science Data, Jan 2025

   Abs DOI 5 citations

   Abstract. The Siberian Arctic is warming rapidly, causing permafrost to thaw and altering the biogeochemistry of aquatic environments, with cascading effects on the coastal and shelf ecosystems of the Arctic Ocean. The Lena River, one of the largest Arctic rivers, drains a catchment dominated by permafrost. Baseline discharge biogeochemistry data are necessary to understand present and future changes in land-to-ocean fluxes. Here, we present a high-frequency 4.5-year-long dataset from a sampling program of the Lena River’s biogeochemistry, spanning April 2018 to August 2022. The dataset comprises 587 sampling events and measurements of various parameters, including water temperature, electrical conductivity, stable oxygen and hydrogen isotopes, dissolved organic carbon concentration and 14C, colored and fluorescent dissolved organic matter, dissolved inorganic and total nutrients, and dissolved elemental and ion concentrations. Sampling consistency and continuity and data quality were ensured through simple sampling protocols, real-time communication, and collaboration with local and international partners. The data are available as a collection of datasets separated by parameter groups and periods at https://doi.org/10.1594/PANGAEA.913197 (Juhls et al., 2020b). To our knowledge, this dataset provides an unprecedented temporal resolution of an Arctic river’s biogeochemistry. This makes it a unique baseline on which future environmental changes, including changes in river hydrology, at temporal scales from precipitation event to seasonal to interannual can be detected.

3. Fluorescence spectroscopy as an indicator tool for pharmaceutical contamination in groundwater and surface water

   Laila Vinther, Mette M. Broholm, Anna-Ricarda Schittich, and 5 more authors

   Chemosphere, Mar 2025

   DOI 13 citations

2024

1. Contaminant mass discharge estimation of a sulfonamide plume by use of hydraulic profiling tool (HPT) and fluorescence techniques

   G.G. Lemaire, M.M. Broholm, U. Wünsch, and 6 more authors

   Journal of Contaminant Hydrology, Nov 2024

   Abs DOI 5 citations

   The contaminant mass discharge is a relevant metric to evaluate the risk that a groundwater plume poses to water resources. However, this assessment is often vitiated by a high uncertainty inherent to the assessment method and often limited number of measurement points to carry out the assessment. Direct-Push techniques in combination with profiling tools and dedicated sampling can be an interesting alternative to increase the measurement point density and hence reduce the mass discharge uncertainty. The main objective of our study was to assess if DP logging and sampling could be employed to get a reasonable estimate of contaminant mass discharge in a large sulfonamide contaminant plume (\textgreater 1500 m wide), compared to a more traditional approach based on monitoring wells. To do so, an Hydraulic Profiling Tool (HPT) logging with a dedicated site calibration was used to estimate the hydraulic conductivity field. The sulfonamide concentrations were inferred from the compound fluorescence properties measured by laboratory spectrofluorometry (λEx / λEm = 255/340 nm) and a dedicated log-log linear regression model. Our results show that HPT-derived hydraulic conductivity values are in good agreement with the monitoring well results, and within the order of magnitude reported in similar studies or indirect geophysical techniques. Fluorescence appears as a powerful proxy for the sulfonamide con­ centration levels. Ultimately, the contaminant mass discharge estimate from HPT and fluorescence techniques lies within a factor 2 from the estimate by monitoring wells, with 549 [274–668] and 776 [695–879] kg/yr respectively. Overall, this study highlights that DP logging tools combined with indirect methods (correlation with fluorescence) could provide a relevant contaminant mass discharge estimate for some optically active substances, given that a proper calibration phase is carried out.

2. Predator-induced defense decreases growth rate and photoprotective capacity in a nitrogen-limited dinoflagellate, Alexandrium minutum

   Jingjing Zhang, Fredrik Ryderheim, Erik Selander, and 2 more authors

   Harmful Algae, Nov 2024

   Abs DOI 7 citations

   Some dinoflagellates produce toxic secondary metabolites that correlate with increased resistance to grazers. The allocation costs of toxin production have been repeatedly addressed, but with conflicting results. Few studies have considered the potential costs of this defense to the photosystem, even though defense toxins (e.g., karlotoxins and brevetoxins) are closely linked to the photoprotective process. Here, we used chemical cues from copepods to induce paralytic shellfish toxin (PST) production in resource-limited Alexandrium minutum and quantitatively determined the growth rate and potential trade-offs with the photosystem process. The results show that grazer-induced, more toxic A. minutum had larger cell volume, lower cell division rate, and lower pigment content under nitrogen-limited conditions than control cells. In addition, predator cues led to a lower relative abundance of photoprotective xanthophylls and a reduced de-epoxidation efficiency of the xanthophyll cycle under high light conditions, reducing the ability of the cells to resist photodamage. Decreased photoprotective capacity may reflect an overlooked defense cost of toxin production.

3. Qualitative variability of dissolved organic matter in the Baltic Sea sediments apparent from fluxes and optical properties

   Alexandra N. Loginova, Urban J. Wünsch, Monika Zabłocka, and 5 more authors

   Frontiers in Marine Science, Sep 2024

   Abs DOI 0 citations

   The release of dissolved organic matter (DOM) from sediments serves as an important part of the carbon cycle. Here, we address pore water DOM quality and its release from shallow sediments (0–10 cm) of the central and southern Baltic Sea - Gdansk, Bornholm, and Eastern Gotland Basins - using excitation–emission matrix spectroscopy and size-exclusion chromatography. DOM release from sediments displayed spatial variability, with diffusive DOC fluxes ranging from 0.02 to 1.06 mmol m −2 d −1 , and basin-averaged fluxes increased in the order Gotland < Bornholm < Gdansk. DOM qualitative characteristics also varied among investigated basins. In the oxygen-limited study sites from the Gdansk Basin, we observed elevated abundances of low apparent molecular weight DOM fraction and proteinaceous-like fluorescent DOM, while in the Bornholm Basin, pore water DOM was generally more humic-like and of higher apparent molecular weight. Pore waters from the deepest study sites in the Gotland Basin were qualitatively very similar to those of the pore waters from the upper sediment layers (0–4 cm) from all other investigated sites, suggesting little organic matter reworking at depth at those stations. Our results suggest that the spatial variability in the magnitude of DOM release may be linked to the qualitative differences of DOM in sediments.

4. Fluorescence Excitation Emission Matrix (EEM) Spectroscopy

   Adam C. Hambly and Urban J. Wünsch

   In Experimental Methods for Membrane Applications in Desalination and Water Treatment, Jan 2024

   Abs DOI 11 citations

   Abstract Water quality is a critical issue for the water industry today, and membrane fi ltration a highly effective treatment used to provide clean water for the global population. Experimental processes and methods are being developed for assessing fouling, scaling, performance and modelling of membrane systems, and research is needed to further improve the sustainability and feasibility of these technologies, and to mitigate the challenges of water scarcity for billions of people, particularly in developing countries. This book aims to address this vital issue by bringing together experts in the fi eld to share their learning, including: Membrane processes: microfi ltration (MF), ultrafi ltration (UF), reverse osmosis (RO), forward osmosis (FO) and membrane distillation (MD)Particulate fouling: silt density index (SDI), modifi ed fouling index (MFI-0.45 and MFI-UF)Inorganic fouling and scaling: assessment, characterization tools and mitigationOrganic fouling: size exclusion chromatography (LC-OCD), fl uorescence spectroscopy (FEEM) and transparent exopolymer particles (TEP)Biological fouling: genomic tools, bacterial growth potential (BGP) of seawater and low-nutrient water and optical coherence tomography (OCT)General applications: membrane autopsy and computational fl uid dynamics (CFD) modelling

2023

1. Lignin phenol quantification from machine learning‐assisted decomposition of liquid chromatography‐absorbance spectroscopy data

   Anders Dalhoff Bruhn, Urban Wünsch, Christopher L. Osburn, and 2 more authors

   Limnology and Oceanography: Methods, Jun 2023

   DOI 4 citations
2. Dissolved organic matter thiol concentrations determine methylmercury bioavailability across the terrestrial-marine aquatic continuum

   Emily Seelen, Van Liem-Nguyen, Urban Wünsch, and 4 more authors

   Nature Communications, Oct 2023

   DOI 75 citations
3. Direct Measurement of Organic Micropollutants in Water and Wastewater Using Fluorescence Spectroscopy

   Lesly Paradina-Fernández, Urban Wünsch, Rasmus Bro, and 1 more author

   ACS ES&T Water, Nov 2023

   Abs DOI 39 citations

   Quantifying organic micropollutants (OMPs) in aquatic environments and assessing their removal by water treatment requires expensive and time-consuming analyses typically using liquid chromatographic separation and tandem mass spectrometry (LC-MS/MS). In this study, we evaluated the potential for detecting fluorescent OMPs via spectroscopy, which is cheap, rapid, and widely accessible. The method involved using a priori PARAFAC models to eliminate interfering background fluorescence emitted by naturally occurring dissolved organic matter. Of 20 screened pharmaceutical OMPs, three (ciprofloxacin, naproxen, and zolpidem) with calculated fluorescence quantum yields 0.14, 0.21, and 0.71, respectively, could be quantified in the low μg L−1 range when added alone or in combination to water samples without any sample pretreatment other than filtration and pH adjustment. Limits of detection for all three OMPs were 1.0−3.3 μg L−1 in surface waters, while in wastewater, they were 0.6− 9.0 μg L−1 for ciprofloxacin and naproxen and 1.0−2.6 μg L−1 for zolpidem. Given the high cost of pharmaceutical analyses and widespread availability of fluorometers, the new approach will improve access to rapid and cost-effective results by supporting dataintensive lab-scale studies, wherein the types of OMPs studied and their concentration ranges are under the control of the analyst.

2022

1. Unified understanding of intrinsic and extrinsic controls of dissolved organic carbon reactivity in aquatic ecosystems

   Martin Berggren, François Guillemette, Magdalena Bieroza, and 12 more authors

   Ecology, Aug 2022

   DOI 69 citations
2. DOM Molecular Weight Fractionation and Fluorescence Quantum Yield Assessment Using a Coupled In-Line SEC Optical Property System

   Blair Hanson, Urban Wünsch, Shelby Buckley, and 5 more authors

   ACS ES&T Water, Oct 2022

   DOI 16 citations
3. Substrate diversity affects carbon utilization rate and threshold concentration for uptake by natural bacterioplankton communities

   J Sjöstedt, UJ Wünsch, and CA Stedmon

   Aquatic Microbial Ecology, Jun 2022

   Abs DOI 3 citations

   Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates — salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr) — or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.

4. Dissolved organic matter characterization in soils and streams in a small coastal low-Arctic catchment

   Niek Jesse Speetjens, George Tanski, Victoria Martin, and 10 more authors

   Biogeosciences, Jul 2022

   Abs DOI 39 citations

   Ongoing climate warming in the western Canadian Arctic is leading to thawing of permafrost soils and subsequent mobilization of its organic matter pool. Part of this mobilized terrestrial organic matter enters the aquatic system as dissolved organic matter (DOM) and is laterally transported from land to sea. Mobilized organic matter is an important source of nutrients for ecosystems, as it is available for microbial breakdown, and thus a source of greenhouse gases. We are beginning to understand spatial controls on the release of DOM as well as the quantities and fate of this material in large Arctic rivers. Yet, these processes remain systematically understudied in small, high-Arctic watersheds, despite the fact that these watersheds experience the strongest warming rates in comparison. Here, we sampled soil (active layer and permafrost) and water (porewater and stream water) from a small ice wedge polygon (IWP) catchment along the Yukon coast, Canada, during the summer of 2018.

5. Electrochemical and microbiological response of exoelectrogenic biofilm to polyethylene microplastics in water

   Song Wang, Mingyi Xu, Biao Jin, and 3 more authors

   Water Research, Mar 2022

   DOI 108 citations
6. When microbial electrochemistry meets UV: The applicability to high-strength real pharmaceutical industry wastewater

   Rusen Zou, Kai Tang, Adam C. Hambly, and 4 more authors

   Journal of Hazardous Materials, Feb 2022

   DOI

2021

1. A simple method to isolate fluorescence spectra from small dissolved organic matter datasets

   Urban J. Wünsch and Kathleen Murphy

   Water Research, Feb 2021

   DOI 74 citations
2. Probing sedimentary DOM in the deepest sector of Earth’s surface

   Tingcang Hu, Min Luo, Urban J. Wünsch, and 5 more authors

   Marine Chemistry, Dec 2021

   Abs DOI

   It has been suggested that hadal trenches are depocenters of organic matter and hotspots for microbial activities. Here, we measured the concentrations of pore-water dissolved organic carbon (DOC) in the seven short cores retrieved from three trenches (i.e., the Mariana Trench, the Mussau Trench, and the New Britain Trench), and analyzed the optical properties of pore-water dissolved organic matter (DOM) from the axis, forearc, and abyssal sediments in the southern Mariana Trench. The positive correlation between the average DOC concentrations and the in-situ total oxygen uptakes among the three trenches suggests that rate of organic matter degradation and redox condition likely control the downcore pore-water DOC concentrations in hadal sediments. Furthermore, analysis of fluorescence DOM reveals a higher carbon-normalized fluorescence of components emitting in the visible (“humic” and “fulvic”-like) at the Mariana Trench axis than at the abyssal plain and forearc. Together with the downcore increase in humification indices and absorbance ratios at the trench axis cores, this points at a significant accumulation of highly degraded, persistent, low-molecular-weight DOM produced by intensified microbial respiration at the trench axis. To our knowledge, this is the first study that examines the features of pore-water DOM in hadal trenches, which provides additional supports for the argument that microbial activities are enhanced at the trench axis and has implication for understanding DOM cycling in deep-sea sediments.

3. Full-Scale Manipulation of the Empty Bed Contact Time to Optimize Dissolved Organic Matter Removal by Drinking Water Biofilters

   Nashita Moona, Andrew Holmes, Urban J. Wünsch, and 2 more authors

   ACS ES&T Water, Apr 2021

   Abs DOI

   A study was conducted at a water treatment plant to optimize parallel rapid gravity biofilters for dissolved organic matter (DOM) removal. The biofilters treat urban and agriculturally impacted river water using a commercial non-adsorptive, expandedclay filter medium. The study aimed to locate the optimal operating conditions via experimental manipulation of the biofilter empty bed contact time (EBCT) during full-scale operation at the plant. During a two-month experiment, contact times in four parallel biofilters were switched to and maintained at 15, 30, 50, and 80 min by manipulating the hydraulic loading on each filter. The removal efficiency of organic matter fractions increased with EBCT for dissolved organic carbon (DOC) and microbial humic-like (F290/420) and protein-like (F280/340) fluorescent organic matter. Other DOM fractions were largely unaffected by biofiltration, or at slightly higher concentrations in the effluent. Protein-like fluorescence is associated with labile organic matter fractions, which are known to be removed poorly by drinking water treatment barriers apart from biological filters. The results suggest that long contact times (\textgreater30 min) have advantages for the operation of some biological filters, especially if placed ahead of barriers that are sensitive to biofouling, e.g., membranes.

2020

1. Mathematical chromatography deciphers the molecular fingerprints of dissolved organic matter

   Urban J. Wünsch and Jeffrey A. Hawkes

   The Analyst, 2020

   Abs DOI 13 citations

   Mathematical chromatography offers information reduction and feature extraction in complex liquid chromatography—mass spectrometry datasets.

2019

1. staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R

   Matthias Pucher, Urban Wünsch, Gabriele Weigelhofer, and 3 more authors

   Water, Nov 2019

   Abs DOI 317 citations

   The roles of dissolved organic matter (DOM) in microbial processes and nutrient cycles depend on its composition, which requires detailed measurements and analyses. We introduce a package for R, called staRdom (“spectroscopic analysis of DOM in R”), to analyze DOM spectroscopic data (absorbance and fluorescence), which is key to deliver fast insight into DOM composition of many samples. staRdom provides functions that standardize data preparation and analysis of spectroscopic data and are inspired by practical work. The user can perform blank subtraction, dilution correction, Raman normalization, scatter removal and interpolation, and fluorescence normalization. The software performs parallel factor analysis (PARAFAC) of excitation–emission matrices (EEMs), including peak picking of EEMs, and calculates fluorescence indices, absorbance indices, and absorbance slope indices from EEMs and absorbance spectra. A comparison between PARAFAC solutions by staRdom in R compared with drEEM in MATLAB showed nearly identical solutions for most datasets, although different convergence criteria are needed to obtain similar results and interpolation of missing data is important when working with staRdom. In conclusion, staRdom offers the opportunity for standardized multivariate decomposition of spectroscopic data without requiring software licensing fees and presuming only basic R knowledge.

2. Temperature-dependent mechanisms of DOM removal by biological activated carbon filters

   Nashita Moona, Urban J. Wünsch, Mia Bondelind, and 4 more authors

   Environmental Science: Water Research & Technology, 2019

   Abs DOI 18 citations

   Physical and chemical adsorption by aged biological active carbon (BAC) filters were observed for some organic matter fractions, and may represent important removal mechanisms during periods of low microbial activity.

3. Emerging patterns in the global distribution of dissolved organic matter fluorescence

   Urban J. Wünsch, Rasmus Bro, Colin A. Stedmon, and 2 more authors

   Analytical Methods, 2019

   Abs DOI 98 citations

   The spectra responsible for natural dissolved organic matter fluorescence in 90 peer-reviewed studies have been compared using new similarity metrics.

2018

1. The Molecular Fingerprint of Fluorescent Natural Organic Matter Offers Insight into Biogeochemical Sources and Diagenetic State

   Urban J. Wünsch, Evrim Acar, Boris P. Koch, and 3 more authors

   Analytical Chemistry, Dec 2018

   Abs DOI 59 citations

   Investigating the biogeochemistry of dissolved organic matter (DOM) requires the synthesis of data from several complementary analytical techniques. The traditional approach to data synthesis is to search for correlations between measurements made on the same sample using different instruments. In contrast, data fusion simultaneously decomposes data from multiple instruments into the underlying shared and unshared components. Here, Advanced Coupled Matrix and Tensor Factorization (ACMTF) was used to identify the molecular fingerprint of DOM fluorescence fractions in Arctic fjords. ACMTF explained 99.84% of the variability with six fully shared components. Individual molecular formulas were linked to multiple fluorescence components and vice versa. Molecular fingerprints differed in diversity and oceanographic patterns, suggesting a link to the biogeochemical sources and diagenetic state ofDOM. The fingerprints obtained through ACMTF were more specific compared to traditional correlation analysis and yielded greater compositional insight. Multivariate data fusion aligns extremely complex, heterogeneous DOM data sets and thus facilitates a more holistic understanding of DOM biogeochemistry.

2. Investigating Fluorescent Organic-Matter Composition as a Key Predictor for Arsenic Mobility in Groundwater Aquifers

   Anna-Ricarda Schittich, Urban J. Wünsch, Harshad V. Kulkarni, and 4 more authors

   Environmental Science & Technology, Oct 2018

   DOI 105 citations
3. Photochemistry Illuminates Ubiquitous Organic Matter Fluorescence Spectra

   K. R. Murphy, S. A. Timko, M. Gonsior, and 3 more authors

   Environmental Science & Technology, Aug 2018

   Abs DOI 189 citations

   Dissolved organic matter (DOM) in aquatic environments forms a vast reservoir of carbon present as a complex super-mixture of compounds. An efficient approach to tracking the production and removal of specific DOM fractions is needed across disciplines, for purposes that range from improving global carbon budgets to optimising water treatment in engineered systems. Although widely used to study DOM, fluorescence spectroscopy has yet to deliver specific fractions with known spectral properties and predictable distributions. Here, we mathematically isolate four visible-wavelength fluorescent fractions in samples from contrasting lake, river, and ocean environments. Using parallel factor analysis (PARAFAC), we show that most measured fluorescence in environmental samples can be explained by ubiquitous spectra with nearly stable optical properties and semi-labile photodegradation rate constants over environmental pH gradients. Sample extraction changed bulk fluorescence spectra but not the number or shape of ...

4. Quantifying the impact of solid-phase extraction on chromophoric dissolved organic matter composition

   Urban J. Wünsch, Jana K. Geuer, Oliver J. Lechtenfeld, and 3 more authors

   Marine Chemistry, Nov 2018

   Abs DOI 71 citations

   Advancing our understanding of the behaviour of dissolved organic matter (DOM) in aquatic environments necessitates efforts to combine complementary analytical data sets. However, some analytical measurements require sample pre-treatment, while others are carried out on bulk water samples, and it remains unclear if the resulting data sets can be compared. Here, we investigated the impact of solid-phase extraction with PPL resins on DOM optical properties. In samples from contrasting Arctic fjords, extraction efficiencies based on optical properties varied spectrally with averages between 31 ± 13% at 411 nm and 40 ± 12% at 363 nm for chromophoric DOM. Similarly, the extraction efficiency for specific fluorescence components varied between 37 ± 16% and 58 ± 18%. Solid-phase extraction also decreased S275–295, fluorescence index, and the freshness index, but increased S350–400, and apparent fluorescence quantum yields, indicating that the extraction process was qualitatively selective. Six fluorescence components identified independently for bulk water and extracted DOM data using parallel factor analysis exhibited different behaviours. Three had identical spectral properties before and after extraction, although their extraction efficiencies varied with water mass characteristics and DOM composition, whereas three other components appeared to change after extraction. With the exception of one fluorescence component, the dynamics of optical properties in bulk water samples were not accurately reflected by DOM extracts. These results indicate that solid-phase extraction imparts a qualitative selectivity that leads to the homogenization of DOM extracts relative to their original samples. Efforts to integrate chemical information from different analytical methods should prioritize comparisons of measurements obtained on the same samples.

2017

1. Unraveling the size‐dependent optical properties of dissolved organic matter

   Urban J. Wünsch, Colin A. Stedmon, Lars J. Tranvik, and 1 more author

   Limnology and Oceanography, Sep 2017

   Abs DOI 50 citations

   The size-dependent optical properties of dissolved organic matter (DOM) from four Swedish lakes were investigated using High Performance Size Exclusion Chromatography (HPSEC) in conjunction with online characterization of absorbance (240–600 nm) and fluorescence (excitation: 275 nm, emission: 300–600 nm). The molecular size of chromophoric DOM (CDOM) was consistently higher than that of fluorescent DOM (FDOM), with an average difference of 0.37 kDa. The relative abundance of FDOM vs. CDOM ranged from 0.3 to 0.7 across lakes, and increased with decreasing average molecular size. Across sites, the CDOM spectral slopes of the large molecular size fraction were highly similar while the low molecular size fraction differed and contributed to different bulk spectral slopes. Our results indicate structural congruence of high molecular size DOM across systems while lake trophic status determined the characteristics of the low size range. Furthermore, the combination of HPSEC and parallel factor analysis (HPSEC-PARAFAC2) allowed the decomposition of DOM fluorescence chromatograms. Three humic-like components and one protein-like component with broadly overlapping molecular size distributions were identified. This overlap provides further evidence for the supramolecular assembly hypothesis since fluorophores, as revealed by PARAFAC2, occur in aggregates of overlapping molecular size. Our results further suggest a link between the molecular size of these fluorophores and the associated supramolecular assemblies. This study demonstrates the potential for HPSEC and novel mathematical approaches to provide unprecedented insights into the relationship between optical and chemical properties of DOM in aquatic systems.

2. The One-Sample PARAFAC Approach Reveals Molecular Size Distributions of Fluorescent Components in Dissolved Organic Matter

   Urban J. Wünsch, Kathleen R. Murphy, and Colin A. Stedmon

   Environmental Science & Technology, Oct 2017

   Abs DOI 212 citations

   Molecular size plays an important role in dissolved organic matter (DOM) biogeochemistry, but its relationship with the fluorescent fraction of DOM (FDOM) remains poorly resolved. Here high-performance size exclusion chromatography (HPSEC) was coupled to fluorescence emission-excitation (EEM) spectroscopy in full spectral (60 emission and 34 excitation wavelengths) and chromatographic resolution (\textless1 Hz), to enable the mathematical decomposition of fluorescence on an individual sample basis by parallel factor analysis (PARAFAC). The approach allowed cross-system comparisons of molecular size distributions for individual fluorescence components obtained from independ- ent data sets. Spectra extracted from allochthonous DOM were highly similar. Allochthonous and autochthonous DOM shared some spectra, but included unique components. In agreement with the supramolecular assembly hypothesis, molecular size distributions of the fluorescence fractions were broad and chromatographically unresolved, possibly representing reoccurring fluorophores forming noncovalently bound assemblies of varying molecular size. Samples shared underlying fluorescence components that differed in their size distributions but not their spectral properties. Thus, in contrast to absorption measurements, bulk fluorescence is unlikely to reliably indicate the average molecular size of DOM. The one-sample approach enables robust and independent cross-site comparisons without large-scale sampling efforts and introduces new analytical opportunities for elucidating the origins and biogeochemical properties of FDOM.

2016

1. Corrigendum: Fluorescence Quantum Yields of Natural Organic Matter and Organic Compounds: Implications for the Fluorescence-based Interpretation of Organic Matter Composition

   Urban J. Wünsch, Kathleen R. Murphy, and Colin A. Stedmon

   Frontiers in Marine Science, Feb 2016

   Abs DOI 7 citations

   A corrigendum on: Fluorescence Quantum Yields of Natural Organic Matter and Organic Compounds: Implications for the Fluorescence-based Interpretation of Organic Matter Composition. by Wünsch UJ, Murphy KR and Stedmon CA (2015) Front. Mar. Sci. 2:98. doi: 10.3389/fmars.2015.00098 The authors wish to include the following corrections to the original article. Some data presented in the published article were inaccurate due to improper instrumental correction factors resulting in incorrect fluorescence intensities. Moreover, we have corrected an error in the aquaDOM toolbox that affected the molar fluorescence and absorbance of organic compounds reported in the original article. Since these issues influenced data reported in all tables and figures, there is a need for this corrigendum. The findings of the original manuscript were unaffected by these issues and remain the same. Corrections are listed below in bold and underlined font. For page numbers, section heading and paragraph numbers please refer to http://dx.doi.org/10.3389/fmars.2015.00098.

2. Seasonal variability of dissolved organic matter in the ColumbiaRiver: In situ sensors elucidate biogeochemical and molecular analyses

   Urban Johannes Wünsch, Boris Peter Koch, Matthias Witt, and 1 more author

   Jun 2016

   Abs DOI 7 citations

   Abstract. The in situ detection of fluorescent dissolved organic matter (FDOM) at high temporal resolution is a powerful proxy to follow dissolved organic matter (DOM) dynamics and DOM flux to coastal oceans when FDOM measurements and dissolved organic carbon (DOC) are highly correlated. Here, we investigated the relationship between FDOM sensors and DOC concentration in the lower Columbia River, USA in spring and summer 2013. Furthermore, we studied the seasonal variability of FDOM and chromophoric DOM (CDOM) optical indices, as well as the seasonal and spatial variability for the molecular characteristics of DOM using ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The fieldwork was conducted concurrently with the operation of in situ sensor platforms that recorded physical and biogeochemical data at hourly intervals. In situ FDOM and DOC concentration was highly correlated and the relationship was used to quantify the river’s DOC flux between March and August 2013. The average flux was 0.93 Gg d−1, which included over three-fold temporal variability (0.45 to 1.62 Gg d−1) associated with seasonal biogeochemical variability. Spectrofluorometry measurements demonstrated that FDOM parameters correlated with major seasonal biogeochemical shifts in the river associated with phytoplankton blooms and river discharge and thus revealed predictable seasonal patterns in DOM quality. FT-ICR-MS analyses elucidated these shifts on the molecular level: the relative abundance of 561 formulas, most of which contained N and S, correlated significantly with chlorophyll a, while 417 formulas (mostly CHO) correlated with CDOM absorbance at 254 nm.

3. Molecular ecological chemistry in Arctic fjords at different stages of deglaciation, Cruise No. MSM56, July 2 - July 25, 2016, Longyearbyen (Svalbard, Norway) - Reykjavík (Iceland)

   B.P. Koch, Uwe John, R. Amann, and 26 more authors

   2016

   Abs DOI 0 citations

   The 22 participating scientists from Germany, Norway, the Netherlands, Denmark, Sweden, Finland and the United States covered scientific expertise in (micro-) biology, chemistry, and oceanography. Apart from aerosol and rainwater collection, which was applied to assess atmospheric deposition, sampling was restricted to the water column. Phyto and zooplankton were sampled by vertical net hauls using a plankton net, multinet and a pump system for the filtration of large water volumes to collect different size classes of phytoplankton, followed by DNA and RNA extraction. Phytoplankton was also characterized and quantified onboard by microscopy and flow cytometry. Primary productivity was assessed in incubations in the isotope container using radiocarbon labels. Clonal cultures were established to identify selected key species. Bacterial abundance, community composition and production were also determined onboard. Chemical sampling and analytical parameters, most of which taken from the CTD water sampler, will be measured back in the home labs. The final dataset will cover inorganic nutrients, oxygen concentration, dissolved inorganic carbon, total alkalinity, He/Ne ratios for the estimation of basal melt water, δ18O for the contribution of meteoric water, particulate and dissolved organic carbon and nitrogen, optical properties (fluorescence), molecular characterization and radiocarbon age of organic matter. A FerryBox system continuously recorded surface water information on turbidity, chlorophyll fluorescence, temperature, salinity, colored dissolved organic matter and salinity. At each station, salinity and temperature profiles were recorded by the CTD system and by profiler deployments, which also recorded the spectral light profile in the water column. The vertical material flux was investigated by the deployment of drifting sediment traps, a camera system and a marine snow catcher.

2015

1. Fluorescence Quantum Yields of Natural Organic Matter and Organic Compounds: Implications for the Fluorescence-based Interpretation of Organic Matter Composition

   Urban J. Wünsch, Kathleen R. Murphy, and Colin A. Stedmon

   Frontiers in Marine Science, Nov 2015

   DOI 176 citations