Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

Comparing black-carbon- and aerosol-absorption-measuring instruments – a new system using lab-generated soot coated with controlled amounts of secondary organic matter

A preprint of the publication can be found here: <a href="https://amt.copernicus.org/preprints/amt-2021-214/">AMTD - Response of black carbon and aerosol absorption measuring instruments to laboratory-generated soot coated with controlled amounts of secondary organic matter (copernicus.org)</a> (doi.org/10.5194/amt-2021-214). The files correspond to the raw data sets used for Figures 3 and 4 of the aforementioned publication. The date and start/stop time of the measurements are listed in the file "overview_measurements".

opencc-zeroApr 2022View details →

Positive associations of soil organic matter and crop yields across a regional network of working farms

The amount of soil organic matter (SOM) is considered a key indicator of soil properties associated with higher fertility. Despite the ubiquity of assumptions surrounding SOM's contributions to soil functioning, we lack quantitative relationships between SOM and yield outcomes on working farms. We quantified the relationship between SOM and yields of corn (Zea mays L.) and silage for a dataset of 170 fields arrayed across 49 farms in a network of growers based in Wisconsin and Minnesota, USA. As SOM concentrations increase, so do yields, though gains start to level off around 4% SOM. When examining the relationship between yield and soil health indicators representative of biologically active carbon pools, we found that mineralizable carbon (min-C) has a stronger relationship with yield than permanganate oxidizable C (POXC). Mineral fertilizer, manure, and SOM had relationships of similar magnitude with yield, highlighting that SOM in combination with exogenous inputs likely plays an important role in driving agricultural productivity in this region. An SOM by crop rotation interaction indicated that the impact of SOM on crop yields varied depending on rotation (continuous corn versus corn in rotation). That is, continuous corn had lower yields than corn in rotation despite higher SOM concentrations. Our findings provide insight into the relationship between indicators of soil health, farm management, and crop yields for a set of working farms and lend support to the goals of soil health initiatives that rest on building SOM in agricultural soils to improve agricultural outcomes.

opencc-by-4.0Jul 2018View details →

Contents of soil organic matter fractions as affected by warming and rain exclusion at a semiarid Mediterranean site

Data and metadata of total, free, intra-aggregate, and mineral-associated organic C and N contents of soils from a dryland ecosystem warming experiment established in Aranjuez, Central Spain.

opencc-zeroMay 2022View details →

Nocturnal dissolved organic matter release by turf algae and its role in the microbialization of reefs

The increased release of dissolved organic matter (DOM) by algae has been associated with the fast but inefficient growth of opportunistic microbial pathogens and the ongoing degradation of coral reefs. Turf algae (consortia of micro- and macroalgae commonly including cyanobacteria) dominate benthic communities on many reefs worldwide. Opposite to other reef algae that predominantly release DOM during the day, turf algae containing cyanobacteria may additionally release large amounts of DOM at night. However, this night-DOM release and its potential contribution to the microbialization of reefs remains to be investigated. We first tested the occurrence of hypoxic conditions at the turf algae-water interface, as a lack of oxygen will facilitate the production and release of fermentation intermediates as night-time DOM. Secondly, the dissolved organic carbon (DOC) release by turf algae was quantified during day- and nighttime, and the quality of day and night exudates as food for bacterioplankton was tested. Finally, DOC release rates of turf algae were combined with estimates of DOC release based on benthic community composition in 1973 and 2013 to explore how changes in benthic community composition affected the contribution of night-DOC to the reef-wide DOC production. A rapid shift from supersaturated to hypoxic conditions at the turf algae-water interface occurred immediately after the onset of darkness, resulting in night-DOC release rates similar to those during daytime. Bioassays revealed major differences in the quality between day and night exudates: Night-DOC was utilized by bacterioplankton two times faster than day-DOC, but yielded a four-times lower growth efficiency. Changes in benthic community composition were estimated to have resulted in a doubling of DOC release since 1973, due to an increasing abundance of benthic cyanobacterial mats (BCMs), with night-DOC release by BCMs and turf algae accounting for >50 % of the total release over a diurnal cycle. Night-DOC released by BCMs and turf algae is likely an important driver in the microbialization of reefs by stimulating microbial respiration at the expense of energy and nutrient transfer to higher trophic levels via the microbial loop and thereby threatens the productivity and biodiversity of these unique ecosystems.

opencc-by-4.0Jun 2022View details →

Organic matter properties of the Rincon del Bonete and Palmar sediment cores (Uruguay)

This database presents the results of organic matter measurements performed on cores collected in  the Rincon del Bonete and Palmar reservoirs (Uruguay) IRMS analyses were conducted on dry sediment for determining organic matter properties, including elemental concentrations (Total Organic Carbon – TOC, Total Nitrogen –TN, both expressed in %) and stable isotope measurements (δ13C and δ15N, expressed in &permil;). These measurements were performed with a continuous flow Elementar® VarioPyro cube analyzer coupled to a Micromass® Isoprime IRMS available at the Alysés platform of the Institut de Recherche pour le Développement (Bondy, France) Sediment cores were collected on 2019/09/01 in the Palmar (PA-02) and Rincon del Bonete (RDB-01) reservoirs (Uruguay). Corresponding authors: anthony.foucher@lsce.ipsl.fr

opencc-by-4.0Jul 2022View details →

Laboratory Assessment of the Impact of Chemical Oxidation, Mineral Dissolution, and Heating on the Nitrogen Isotopic Composition of Fossil-bound Organic Matter

Results of laboratory experiments reported in the manuscript "Laboratory Assessment of the Impact of Chemical Oxidation, Mineral Dissolution, and Heating on the Nitrogen Isotopic Composition of Fossil-bound Organic Matter", published in the journal Geochemistry, Geophysics, Geosystems

opencc-by-4.0Aug 2022View details →

Molecular Level Estimation of the Composition and Fate of Dissolved Organic Matter in Fire-Impacted Temperate and Subtropical Peatlands

Calculated values of optical (UV-visible and fluorescence) spectroscopy parameters and molecular formulas determined by ultrahigh resolution mass spectrometry for dissolved organic matter (DOM) in porewaters from a temperate and sub-tropical peatland. These data were used to generate figures in a manuscript submitted to the Journal of Geophysical Research - Biogeosciences.

opencc-by-4.0Aug 2022View details →

Data Repository for Peatland Organic Matter Quality Varies with Latitude as Confirmed from FTIR and Ramped Pyrolysis Oxidation

Data information: This is the dataset for a study by Sparrow et al. comparing the organic matter quality of peat cores in four climates (tropical, subtropical, boreal, and polar) using multiple analytical approaches. Data for 16 samples (samples from 4 depths in each of the 4 cores) are presented in the study and all relevant and necessary data are published in this repository: <ul> <li>14C content and d13C results for 1) bulk and 2) ramped pyrolysis oxidation splits and standard materials</li> <li>Elemental analysis results (%C, %N, C:N)</li> <li>FTIR spectra from 650-4000 cm-1</li> <li>Ramped pyrolysis oxidation run data (time, sample oven temperature, baseline-corrected CO2 concentration)</li> </ul> Sample information: <ul> <li>The Tropical peat samples were collected from a core obtained in November 2011, “MDM11-2A,” (4.3727°N, 114.3550°E) in the Ulu Mendaram Conservation Area in the Belait District of Brunei Darussalem, northwest Borneo.</li> <li>The Subtropical peat samples were collected from the “Lox3” core (26.597°N, 80.357°W) in October 2015 from the Loxahatchee National Wildlife Refuge, Florida.</li> <li>The Boreal peat samples were collected from the “T3F” core (47.5063°N, 93.4527°W) from S1 Bog in July 2012 from the Marcell Experimental Forest, near Grand Rapids, Minnesota.</li> <li>The Polar peat samples were collected from the “CPP” core (68.3531°N, 19.0473°E) in June 2012 from Stordalen Mire, a peat plateau underlain by discontinuous permafrost near Abisko, Sweden.</li> </ul>

Data for: Transformation of dissolved organic matter by two Indo-Pacific sponges

Dissolved organic matter (DOM) is the largest organic carbon reservoir in the ocean and an integral component of biogeochemical cycles. The role of free-living microbes in DOM transformation has been studied thoroughly, whereas little attention has been directed towards the influence of benthic organisms. Sponges are efficient filter feeders and common inhabitants of many benthic communities circumglobally. In our study, we investigated how two tropical coral reef sponges shape marine DOM. We compared bacterial abundance, inorganic and organic nutrients in off reef, sponge inhalant, and sponge exhalant water of Melophlus sarasinorum and Rhabdastrella globostellata. DOM and bacterial cells were taken up, and dissolved inorganic nitrogen was released by the two Indo-Pacific sponges. Both sponge species utilized a common set of 142 of a total of 3040 compounds detected in DOM on a molecular formula level via ultrahigh-resolution mass spectrometry. In addition, species-specific uptake was observed, likely due to differences in their associated microbial communities. Overall, the sponges removed presumably semi-labile and semi-refractory compounds from the water column, thereby competing with pelagic bacteria. Within minutes, sponge holobionts altered the molecular composition of surface water DOM (inhalant) into a composition similar to deep-sea DOM (exhalent). The apparent radiocarbon age of DOM increased consistently from off reef and inhalant to exhalant by about 900 14C years for M. sarasinorum. In the pelagic, similar transformations require decades to centuries. Our results stress the dependence of DOM lability definition on the respective environment and illustrate that sponges are hotspots of DOM transformation in the ocean. Here, we provide the data from this study. The four tables contain the metadata, bulk measurements of dissolved organic carbon (DOC), total dissolved nitrogen, NOx, and radiocarbon dating of DOC, bacterioplankton abundances measured with a flow cytometer, and relative peak intensities of molecular formulas obtained through Fourier-transform ion cyclotron resonance mass spectrometry and the online tool ICBM-OCEAN.

Phytoplankton assemblage shifts with dissolved organic matter properties: a functional perspective for sentinel lakes

1. Climate change is altering both dissolved organic matter (DOM) properties and phytoplankton dynamics in lakes. High-altitude lakes are good sentinels of global change. However, their value as sentinels depends on how well we understand their functioning. This study analyzed physical, chemical, and biological data during three pre-defined periods running from complete ice-cover right to the end of the ice-free season, in a high-altitude oligotrophic lake. A functional approach was used to assess how relationships between DOM and the planktonic community vary over time. 2. Phytoplankton functional change was found to occur with shifts in dissolved organic matter. During the ice-influenced period, from February to the end of the thaw, the phytoplankton community was dominated by small autotrophs and mixotrophic flagellates and DOM from sediment and terrestrial origin dominated the DOM pool of the lake. Phytoplankton diversity and richness increased during the post-snowmelt overturn period, when terrestrial DOM dominated the DOM pool. Finally, large siliceous autotrophs, competitive under low nitrogen concentrations and high temperature, dominated almost exclusively during the late summer period. Increased phytoplankton biomass meant that phytoplankton-derived DOM was dominant during the late summer period. 3. These phenological changes in the phytoplankton community resulted in functional shifts at the base of the food web. Based on the relationships between the variables in the study, it can be deduced that the nature of the relationship between phytoplankton and bacteria progressively shifted from strong top-down control exerted by phytoplankton over bacteria toward predominantly bottom-up control at the end of the ice-free season. 4. Synthesis. Using a field survey starting from complete ice-cover and lasting right to the end of the ice-free season in a sentinel lake, we show seasonal shifts in the link between dissolved organic matter properties and plankton community traits. Differences in environmental conditions and DOM origin explained variation in phytoplankton community structure and function, pointing to seasonal shifts in microbial food web interactions. Our research suggests that, under climate change, the balance between mixotrophy and autotrophy and the control exerted by phytoplankton over bacterioplankton will change in oligotrophic high-altitude lakes with large, vegetated catchments.

Unique microbiome in organic matter-polluted urban rivers

Approximately half of the global annual production of wastewater is released untreated into aquatic environments, which results in worldwide organic matter pollution in urban rivers, especially in highly populated developing countries. Nonetheless, information on microbial community assembly and assembly-driving processes in organic matter-polluted urban rivers remains elusive. In this study, a field study based on water and sediment samples collected from 200 organic matter-polluted urban rivers of 82 cities in China and Indonesia is combined with laboratory water-sediment column experiments. Our findings demonstrate a unique microbiome in these urban rivers. Among the community assembly-regulating factors, both organic matter and geographic conditions play major roles in determining prokaryotic and eukaryotic community assemblies, especially regarding the critical role of organic matter in regulating taxonomic composition. Using a dissimilarity-overlap approach, we found universality in the dynamics of water and sediment community assembly in organic matter-polluted urban rivers, which is distinctively different from patterns in eutrophic and oligotrophic waters. The prokaryotic and eukaryotic communities are dominated by deterministic and stochastic processes, respectively. Interestingly, water prokaryotic communities showed a three-phase cyclic succession of the community assembly process before, during, and after organic matter pollution. Our study provides the first large-scale and comprehensive insight into the prokaryotic and eukaryotic community assembly in organic matter-polluted urban rivers and supports their future sustainable management.

opencc-by-4.0Sep 2022View details →

The frequent occurrence and metabolic versatility of Marinifilaceae bacteria involved in organic matter mineralization as a key member in global deep sea

Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on the global scale. Microorganisms play an important role in mineralizing them therein, yet to identify in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found the family Marinifilaceae occurred as one of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea of both marginal and oceanic areas. This taxa is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups based on the phylogenomic tree. We described the metabolic features and in situ metabolizing activities of different MF subgroups via the metagenomic and metatranscriptomic data. One representative subgroup MF-2 dominated plant detritus-enriched cultures and specialized in polysaccharide degradation and lignin oxidation. Intriguingly, they encode nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, those dominating the animal tissue-supported microbiomes were more diverse and formed three subgroups, which distinguished themselves from MF-2 in carbon and nitrogen metabolisms. Despite these metabolic divergences of MF lineages, they harbored anaerobic processes for energy conservation via organic fermentation, anaerobic respiration via iron and manganese reduction, and/or dimethyl sulfoxide reduction. These results highlight the role of Marinifilaceae bacteria neglected before in organic matter mineralizing in marine environments coupling carbon and nitrogen cycling with metals and other elements.

Oxygen availability regulates the quality of soil dissolved organic matter by mediating microbial metabolism and iron oxidation

Dissolved organic matter (DOM) plays a vital role in biogeochemical processes and in determining the responses of soil organic matter (SOM) to global change. Although the quantity of soil DOM has been inventoried across diverse spatio-temporal scales, the underlying mechanisms accounting for variability in DOM dynamics remain unclear, especially in upland ecosystems. Here, a gradient of SOM storage across twelve croplands in northeast China was used to understand links between DOM dynamics, microbial metabolism, and abiotic conditions. We assessed the composition, biodegradability and key biodegradable components of DOM. In addition, SOM and mineral-associated organic matter (MAOM) composition, soil enzyme activities, oxygen availability, soil texture, iron (Fe), Fe-bound organic matter and nutrient concentrations were quantified to clarify the drivers of DOM quality (composition and biodegradability). The proportion of biodegradable DOM increased exponentially with decreasing initial DOM concentration due to larger fractions of depolymerized DOM that was rich in small-molecular phenols and proteinaceous components. Unexpectedly, the composition of DOM was decoupled from that of SOM or MAOM, but significantly related to enzymatic properties. These results indicate that microbial metabolism exhibited a dominant role in DOM generation. As DOM concentration declined, increased soil oxygen availability regulated DOM composition and enhanced its biodegradability mainly through mediating microbial metabolism and Fe oxidation. The oxygen-induced oxidation of Fe(II) to Fe(III) removed complex DOM compounds with large molecular weight. Moreover, increased oxygen availability stimulated oxidase-catalyzed depolymerization of aromatic substances, and promoted production of protein-like DOM components due to lower enzymatic C/N acquisition ratio. As global changes in temperature and moisture will have large impacts on soil oxygen availability, the role of oxygen in regulating DOM dynamics highlights the importance of integrating soil oxygen supply with microbial metabolism and Fe redox status to improve model predictions of soil carbon under climate change.

opencc-by-4.0Apr 2024View details →

Data set for spectral and FT-ICR-MS analysis of dissolved organic matter in sediments of the New Britain Trench axis station

数据集包括原始数据和简单处理所需的数据、图表和文章。   表格包含样品数量、收集深度、样品名称以及相应光谱和 FT-ICR-MS 数据的名称。   例如,光谱数据包括荧光相对强度、荧光指数,而 FT-ICR-MS 光谱数据包括化合物类型相对强度以及化学式、元素比、等效双键数 (DBE) 和每个样品的芳香指数 (AImod)。

opencc-by-4.0May 2024View details →

Combined data file for Jokinen et al. "Terrestrial organic matter input drives sedimentary trace metal sequestration in a human-impacted boreal estuary", Science of the Total Environment 717, 2020

The datafile contains all the new raw data presented in the figures in the publication.

opencc-by-4.0Jul 2024View details →

Dataset for Quantifying Dissolved Organic Matter Scaling Relationships and Trends in Watersheds

This updated dataset explores the relationship between species richness (i.e., compound metrics) and watershed characteristics using various environmental datasets and data-driven methods. The repository includes data and associated links, notes on curating the data (e.g., graphics, slides), and data analysis scripts to understand species-watershed relationships.

opencc-by-4.0Jul 2018View details →

Quality of free soil organic matter fraction as affected by warming and rain exclusion at a semiarid Mediterranean site

Data and metadata of nuclear magnetic resonance (NMR) of free organic matter fraction of soils from a dryland ecosystem warming experiment established in Aranjuez, Central Spain.

opencc-by-4.0Jul 2018View details →

Contents of soil organic matter fractions as affected by warming and rain exclusion at a semiarid Mediterranean site

Data and metadata of total, free, intra-aggregate, and mineral-associated organic C and N contents of soils from a dryland ecosystem warming experiment established in Aranjuez, Central Spain.

opencc-zeroDec 2017View details →

Data from: Organic matter loading by hippopotami causes subsidy overload resulting in downstream hypoxia and fish kills

Organic matter and nutrient loading into aquatic ecosystems affects ecosystem structure and function and can result in eutrophication and hypoxia. Hypoxia is usually attributed to anthropogenic pollution and is rarely documented in unpolluted systems, particularly in rivers. Here we show that organic matter loading from hippopotami causes the repeated occurrence of hypoxia in the Mara River, East Africa. We documented 49 high flow events over three years that caused dissolved oxygen decreases, including 13 events resulting in hypoxia, and 9 fish kills over five years. Evidence from experiments and modeling demonstrates a strong mechanistic link between the flushing of hippo pools and decreased dissolved oxygen. This phenomenon may have been more widespread throughout Africa before hippo populations were severely reduced. Frequent hypoxia may be a natural part of tropical river ecosystem function, which directly challenges our notions of the reference state of rivers in the absence of human influence.