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opencc-zeroDec 2018View details →

Data from: Degradation of internal organic matter is the main control on pteropod shell dissolution after death

The potential for preservation of thecosome pteropods is thought to be largely governed by the chemical stability of their delicate aragonitic shells in seawater. However, sediment trap studies have found that significant carbonate dissolution can occur above the carbonate saturation horizon. Here we present the results from experiments conducted on two cruises to the Scotia Sea to directly test whether the breakdown of the organic pteropod body influences shell dissolution. We find that, on the timescales of three to thirteen days, the oxidation of organic matter within the shells of dead pteropods is a stronger driver of shell dissolution than the saturation state of seawater. Three to four days after death, shells became milky white and nano‐SEM images reveal smoothing of internal surface features and increased shell porosity, both indicative of aragonite dissolution. These findings have implications for the interpretation of the condition of pteropod shells from sediment traps and the fossil record, as well as for understanding the processes controlling particulate carbonate export from the surface ocean.

opencc-zeroDec 2017View details →

Data from: Stable isotope signatures of underground seedlings reveal the organic matter gained by adult orchids from mycorrhizal fungi

1.Orchids produce dust seeds dependent on the provision of organic carbon by mycorrhizal fungi for their early development stages. Hence, all chlorophyllous orchids experience a dramatic switch in trophic strategies from initial mycoheterotrophy to either autotrophy or partial mycoheterotrophy during ontogeny. Yet, the degree to which partially mycoheterotrophic orchids gain carbon from their mycorrhizal fungi is unclear based on existing approaches. 2.Here, we propose a novel approach to quantify the fungal-derived organic matter gain of chlorophyllous mature orchids mycorrhizal with rhizoctonia fungi using the stable isotope signatures of their fully mycoheterotrophic (FMH) seedlings in a linear two-source mixing model. 3.We conducted a field germination experiment with seven orchid species and measured carbon, nitrogen and hydrogen stable isotope natural abundances and nitrogen concentrations of mature orchids, underground seedlings and autotrophic references. 4.After in situ burial for 19 – 30 months, germination rates varied considerably among five orchid species and failed for two. On average, underground seedlings were enriched in 13C and 15N relative to mature orchids and had higher nitrogen concentrations. Using the mean enrichment factors ε13C and ε2H of seedlings as FMH endpoint, the organic matter gain derived by mature orchids from mycorrhizas was ca. 20%. 5.Chlorophyllous orchids mycorrhizal with rhizoctonias are predisposed to partially mycoheterotrophic nutrition due to their initially mycoheterotrophic seedling stage. We show that the carbon and hydrogen isotope abundances of underground seedlings can be used in an improved mixing-model to identify a significant proportion of fungal-derived organic matter in mature orchids.

opencc-zeroJun 2021View details →

Bulk and amino acid nitrogen specific isotope data from particulate organic matter and mesozooplankton (1000-2000 µm) from the Mekong River plume and southern South China Sea

The mean trophic position (TP) of mesozooplankton largely determines how much mass and energy is available for higher trophic levels like fish. Unfortunately, the ratio of herbivores to carnivores in mesozooplankton is difficult to identify in field samples. Here we investigated changes in the mean TP of mesozooplankton in a highly dynamic environment encompassing four distinct habitats in the southern South China Sea: the Mekong River plume, coastal upwelling region, shelf waters, and offshore oceanic waters. We used a set of parameters derived from bulk and amino acid nitrogen stable isotopes from particulate organic matter (POM) and four mesozooplankton size fractions to identify changes in the nitrogen source and structure of the planktonic food web across these habitats. We found clear indications of a shift in N sources for biological production from nitrate in near-coastal waters towards an increase in diazotroph-N inputs in oceanic waters where diazotrophs shaped the phytoplankton community. The shift in N source was accompanied by a lengthening of the food chain (increase in the TP), which may provide further support for the connection between diazotrophy and the indirect routing of N through the marine food web. Our combined bulk and amino acid δ15N approach also allowed us to estimate the trophic enrichment (TE) of mesozooplankton across the entire regional ecosystem. When put in the context of literature values, our high TE of 5.1‰ suggested a link between ecosystem heterogeneity and the less efficient transfer of mass and energy across trophic levels.

opencc-by-4.0Jul 2021View details →

Effects of Application of Recycled Chicken Manure and Spent Mushroom Substrate on Organic Matter, Acidity, and Hydraulic Properties of Sandy Soils

This study aimed at examining the effects of long-term application of chicken manure (CM) and spent mushroom substrate (SMS) on organic matter accumulation, acidity, and hydraulic properties of soil. Two podzol soils with sandy texture in Podlasie Region (Poland) were enriched with recycled CM (10 Mg ha􀀀1) and SMS (20 Mg ha􀀀1), respectively, every 1–2 years for 20 years. The application of CM and SMS increased soil organic matter content at the depths of 0–20, 20–40, and 40–60 cm, especially at 0–20 cm (by 102–201%). The initial soil pH increased in the CM- and SMS-amended soil by 1.7–2.0 units and 1.0–1.2 units, respectively. Soil bulk density at comparable depths increased and decreased following the addition of CM and SMS, respectively. The addition of CM increased field water capacity (at –100 hPa) in the range from 45.8 to 117.8% depending on the depth within the 0–60 cm layer. In the case of the SMS addition, the value of the parameter was in the range of 42.4–48.5% at two depths within 0–40 cm. Depending on the depth, CM reduced the content of transmission pores (>50 m) in the range from 46.3 to 82.3% and increased the level of residual pores (<0.5 m) by 91.0–198.6%. SMS increased the content of residual pores at the successive depths by 121.8, 251.0, and 30.3% and decreased or increased the content of transmission and storage pores. Additionally, it significantly reduced the saturated hydraulic conductivity at two depths within 0–40 cm. The fitted unsaturated hydraulic conductivity at two depths within the 0–40 cm layer increased and decreased in the CM- and SMS-amended soils, respectively. The results provide a novel insight into the application of recycled organic materials to sequester soil organic matter and improve crop productivity by increasing soil water retention capacity and decreasing acidity. This is of particular importance in the case of the studied low-productivity sandy acidic soils that have to be used in agriculture due to limited global land resources and rising food demand.

Figure 4 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 4. Regression analyses of species richness from the various distance intervals in Howard's Waterfall Cave, Georgia.

Figure 6 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 6. Regression analyses of total Collembola abundance from the various distance intervals in Howard's Waterfall Cave, Georgia.

Figure 3 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 3. Regression of total invertebrate abundance and % total organic matter (% TOM) from the various distance interval in Cave Springs Cave, Alabama.

Figure 1 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 1. Our ramp-pitfall trap without styrofoam plate and bait. Plastic container dimensions (width and height 18 cm), openings to container (width 8 cm, height 7 cm), ramps (8 cm, 19 cm, and slanted side 18 cm).

Figure 2 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 2. Regression of total invertebrate abundance and % total organic matter (% TOM) from the various distance intervals in Anvil Cave, Alabama.

Figure 5 in Terrestrial macroinvertebrates captured with a baited ramp-pitfall trap from five limestone caves in North Alabama and Georgia (USA) and their association with soil organic matter

Figure 5. Regression analyses of total invertebrate abundance from the various distance intervals in Howard's Waterfall Cave, Georgia.

opencc-by-4.0Aug 2021View details →

Observed and predicted organic matter data

Punctual soil organic matter data observed in the field and predicted with prediction models fitted by Partial Least Squares Multiple Linear Regression - PLS.

opencc-zeroAug 2021View details →

Isotopic data of kelps and particulate organic matter (POM) from relevant studies and estimated contributions of kelps to local consumers

Kelp forests are highly productive coastal habitats that serve as biodiversity hotspots and provide valuable ecosystem services. Despite being one the largest marine biomes, kelp forests have been drastically understudied relative to other marine systems. Notably, while the role of kelp as habitat-forming, or 'foundation species', is well-documented, a comprehensive understanding of kelp forest food web structure is lacking, particularly regarding the importance of kelp-derived energy/nutrients to consumers. Here, we provide a biogeographic perspective on the energetic underpinning of kelp forests based on published literature. We targeted studies which used geochemical proxies – stable isotope analysis – to examine the transfer of carbon from kelp to local consumers. These studies (n=94) were geographically skewed, with >40% from Northern European Seas and Temperate Northeast Pacific. Quantitative estimates for the percentage of kelp energy (or kelp+macroalgae if sources were pooled) incorporated by local consumers came from 43 publications, which studied 141 species and 35 broader taxonomic groups. We examined these data for trends among functional groups and across upwelling regimes. No patterns are evident at present, perhaps due to the paucity or variability of available data. However, energetic subsides from kelps clearly support a wide range of diverse taxa around the globe. We also characterized biogeographic patterns in d13C values of kelps and particulate organic matter (POM, a phytoplankton proxy), to evaluate potential limitations of stable isotope analysis in disentangling the relative contributions of pelagic vs. benthic resources to coastal food webs. Globally, kelps and POM differed by >4.5‰, but there was substantial variation among regions and kelp species. Accordingly, we discuss advances in stable isotope techniques which are facilitating more precise analysis of these complex energetic pathways. We end by proposing four main avenues of critical future research that will shed light on the resilience of these communities to global change.

opencc-zeroSep 2021View details →

Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas

Populations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. Changing these patterns of OM and nutrients transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.

opencc-zeroOct 2021View details →

Natural history of model organisms: the secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology

<ol> <li>Model organisms such as Drosophila melanogaster have been key tools for advancing our fundamental and applied knowledge in biological and biomedical sciences. However, model organisms have become intertwined with the idea of controlled and stable laboratory environments, and their natural history has been overlooked.</li> <li>In holometabolous insects, lack of natural history information on larval ecology has precluded major advances in the field of developmental ecology, especially in terms of manipulations of population density early in life (i.e., larval density). This is because of relativistic and to some extent, arbitrary methodologies employed to manipulate larval densities in laboratory studies. As a result, these methodologies render comparisons between species impossible, precluding our understanding of macroevolutionary responses to population densities during development that can be derived from comparative studies.</li> <li>We recently proposed a new conceptual framework to address this issue and here, we provide the first natural history investigation of Drosophila melanogaster larval density under such framework. First, we characterised the distribution of larval densities in wild population of D. melanogaster using rotting apples as breeding substrate in a suburban area in Sweden.</li> <li>Next, we compiled the commonly used methodologies for manipulating larval densities in laboratory studies from the literature and found that the majority of laboratory studies did not manipulate larval densities below or above the densities observed in nature, suggesting that we have yet to study true life-history and physiological responses to low and high population densities during D. melanogaster development.</li> <li>This is, to our knowledge, the first direct natural history account of larval density in nature for this model organism. Our study paves the way for a more integrated view of organismal biology which re-incorporates natural history of model organisms into hypothesis-driven research in developmental ecology.</li> </ol>

opencc-by-4.0Oct 2021View details →

Dataset: A model of tension-induced fiber growth predicts white matter organization during brain folding

This dataset contains models, MRI data, and code associated with "A model of tension-induced fiber growth predicts white matter organization during brain folding" in Nature Communications (accepted 27 Oct 2021). Included files: <ol> <li>NatCommMRIdata.zip - MRI data and associated MATLAB code for analysis of each subject</li> <li>folding_with_fibers.mph - model file used to generate results in Main Text. Modifiable parameters include stress-dependent fiber elongation rate, initial fiber volume fractions, initial geometry, and cortical growth rate. Compatible with COMSOL Multiphysics (version 5.3).</li> <li>folding_with_fibersECM.mph - model file corresponding to Supplementary Fig. 2. Compatible with COMSOL Multiphysics (version 5.3).</li> <li>folding_with_fibers_linear.mph - model file corresponding to Supplementary Fig. 3. Compatible with COMSOL Multiphysics (version 5.3).</li> </ol> <ol> </ol>

opencc-zeroOct 2021View details →

Data from: Living, dead, and absent trees - How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline?

Mountain birch forests (B. pubescens Ehrh. ssp. czerepanovii) at the subarctic treeline not only benefit from global warming, but are also increasingly affected by caterpillar outbreaks from foliage-feeding geometrid moths. Both of these factors have unknown consequences on soil organic carbon (SOC) stocks and biogeochemical cycles. We measured SOC stocks down to the bedrock under living trees and under two stages of dead trees (12 and 55 years since moth outbreak) and treeless tundra in northern Finland. We also measured in-situ soil respiration, potential SOC decomposability, biological (enzyme activities, microbial biomass), and chemical (N, mineral N, pH) soil properties. SOC stocks were significantly higher under living trees (4.1±2.1 kg m²) than in the treeless tundra (2.4±0.6 kg m²), and remained at an elevated level even 12 (3.7±1.7 kg m²) and 55 years (4.9±3.0 kg m²) after tree death. Effects of tree status on SOC stocks decreased with increasing distance from the tree and with increasing depth, i.e. a significant effect of tree status was found in the organic layer, but not in mineral soil. Soil under living trees was characterized by higher mineral N contents, microbial biomass, microbial activity, and soil respiration compared with the treeless tundra; soils under dead trees were intermediate between these two. The results suggest accelerated organic matter turnover under living trees but a positive net effect on SOC stocks. Slowed organic matter turnover and continuous supply of deadwood may explain why SOC stocks remained elevated under dead trees, despite the heavy decrease in aboveground C stocks. We conclude that the increased occurrence of moth damage with climate change would have minor effects on SOC stocks, but ultimately decrease ecosystem C stocks (49% within 55 years in this area), if the mountain birch forests will not be able to recover from the outbreaks.

opencc-by-4.0Nov 2022View details →

Data for the article "Quantitative Impact of Organic Matter and Soil Moisture on Permafrost"

Data for the article "Quantitative Impact of Organic Matter and Soil Moisture on Permafrost"

opencc-by-4.0Oct 2022View details →

Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks

This repository hosts the code to run the analysis presented in  "Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks"  by Catalan et al., Ecosystems, 2022. DOI: https://doi.org/10.1007/s10021-022-00802-4 The code has been tested on Matlab R2019b. Run the Main.m code to produce the results of Figure 3 and 4 of the paper. Each simulation takes about 8 hours on a standard Desktop computer.

opencc-by-4.0Dec 2022View details →

Virus infection of phytoplankton increases average molar mass and reduces hygroscopicity of aerosolized organic matter

Raw data pertaining to the manuscript titled "Virus infection of phytoplankton increases average molar mass and reduces hygroscopicity of aerosolized organic matter."