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Does long-term soil warming affect microbial element limitation? A test by short-term assays of microbial growth responses to labile C, N and P additions

Increasing global temperatures have been reported to accelerate soil carbon (C) cycling but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0–10, 10–20 cm) in control and warmed (>14 yrs warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 hours. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration – though easy and cheap to measure – is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

Anonymized Survey Responses

This file contains the survey questions, 101 participants' responses to the survey questions and information on coding.

Data from: Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep

Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations. We tracked the spread of a novel strain of Mycoplasma ovipneumoniae in a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) in the Mojave desert to investigate how variation in connectivity among populations influenced disease outcomes. M. ovipneumoniae was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling. Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen. Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.

Wildlife response to disturbances in agent-based models: synthesis on current development and challenges (Systematic Review)

This dataset was obtained from a systematic screening of 124 articles presenting agent-based models of wildlife response to disturbances. It is part of a manuscript for submission to the journal Methods in Ecology and Evolution. The manuscript is entitled: Wildlife response to disturbances in agent-based models: synthesis on current development and challenges.

Aesthetic Responses to the Covid-19 Crisis: The corona performance No Problama Video/Audio Documentation

The video files document the artistic performance No Problama, a coronavirus story from Homborsund created during the Covid-19 crisis in Grimstad, Norway in 2021. Each video presents components of the performance which are described and analysed in the article Aesthetic responses to the Covid-19 pandemic: The Corona-performance No Problama 2021  which belongs to the Routledge Open Access Collection Art and Crisis. All participants have given their written consent for the publication.

Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration

To explore the diversity of microbial growth responses, we have compiled 247 measurements of half-saturation concentrations K and maximum growth rates gmax from previously-published studies (see Methods). The data includes a wide range of resources, including sources of carbon, nitrogen, phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate having the largest number of measurements due to their emphasis in marine and laboratory systems. Organisms include prokaryotes and eukaryotes as well as autotrophs and heterotrophs. This data has been analyzed in a companion research article. For data plots and a discussion of results, please refer to: <div class="csl-bib-body"> <div class="csl-entry">Fink, Justus Wilhelm, Noelle A. Held, and Michael Manhart. "Microbial Population Dynamics Decouple Growth Response from Environmental Nutrient Concentration." Proceedings of the National Academy of Sciences 120, no. 2 (January 10, 2023). <a href="https://doi.org/10.1073/pnas.2207295120">https://doi.org/10.1073/pnas.2207295120</a>.</div> </div>

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors - Dataset

Dataset used from the publication "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab" published in  Cell. 2017 Nov 2;171(4):934-949.e16.  doi: 10.1016/j.cell.2017.09.028. Epub 2017 Oct 12.

Response of the Snowball Earth Climate to Orbital Forcing at High CO2 Level

CAM3&CLM3 simulation results that support the findings of this study are archived here.

Long-term responses to large-scale disturbances: Spatiotemporal variation in gastropod populations and communities

The Anthropocene is characterized by complex, primarily human-generated, disturbance regimes that include combinations of long-term press (e.g. climate change, pollution) and episodic pulse (e.g. cyclonic storms, floods, wildfires, land use change) disturbances. Within any regime, disturbances occur at multiple spatial and temporal scales, creating complex and varied interactions that influence spatiotemporal dynamics in the abundance, distribution, and biodiversity of organisms. Moreover, responses to disturbance are context-dependent, with the legacies of previous disturbances affecting responses to ensuing perturbations. We use three decades of annual data to evaluate the effects of repeated pulse disturbances and global warming on gastropod populations and communities in Puerto Rico at multiple spatial scales. More specifically, we quantify (1) the relative importance of large-scale and small-scale aspects of disturbance on variation in abundance, biodiversity, and species composition; and (2) the spatial scales at which populations and communities integrate information in the spatially heterogenous environments created by disturbances. Gastropods do not exhibit consistent decreases in abundance or biodiversity in association with global warming: abundance for many species has increased over time and species richness does not evince a temporal trend. Nonetheless, gastropods are sensitive to hurricane severity, spatial environmental variation, and successional trajectories of the flora. In addition, they exhibit context-dependent (i.e. legacy effects) responses that are scale-dependent. The Puerto Rican biota has evolved in a disturbance-mediated system. This historical exposure to repeated, severe hurricane-induced disturbances has imbued the biota with high resistance and resilience to the current disturbance regime, resulting in an ability to persist or thrive under current environmental conditions. Nonetheless, these ecosystems may yet be threatened by worsening direct and indirect effects of climate change. In particular, more frequent and severe hurricanes may prevent the establishment of closed-canopy forests, negatively impacting populations and communities that rely on these habitats.

Data from: Physiological response of mature red spruce trees to partial and complete sapwood severing

Drought frequency and severity are projected to increase in many regions of the world, yet it remains unclear how mesic forest trees will respond to these novel climate conditions. Experimentally imposing drought in forests at the stand scale is logistically difficult, however, disturbing the hydraulic functioning of individual trees can induce severe water stress and may inform how large trees respond to future droughts. In this study, we manipulated water availability of red spruce (Picea rubens Sarg.) trees by partially or completely severing sapwood, and measured impacts on water relations and photosynthetic efficiency over four months. Trees with total sapwood severed (TOT) experienced a rapid 96.7% reduction in daily sap flow whereas trees with only partial sapwood severed (PAR; estimated 2 – 5% sapwood remaining) and no sapwood severed (CON; phloem girdled) experienced average reductions of 74.3% and 4.6%, respectively. Sapwood severing in TOT trees resulted in declining midday shoot water potential compared to PAR and CON trees, but TOT trees did not surpass the water potential indicative of 50% loss of conductivity until approximately 12 weeks post treatment. At seven weeks post treatment, TOT trees had 6.8 times lower midday stomatal conductance than PAR and CON trees. Furthermore, branch- and crown-wood water potentials reached extreme values (below measurement threshold of -7.7 MPa) in TOT trees by the time of tree harvest at 18 weeks but remained high and did not differ between PAR and CON trees. Our results indicate that with minimal intact sapwood, PAR trees still had sufficient hydraulic functioning to avoid water stress, while TOT trees had temporary resistance to water stress likely associated with declines in carbon sequestration and growth. These findings advance our understanding of how red spruce may physiologically respond to periods of water stress in future climates.

Room Impulse Responses (RIRs) for B-format recordings

Room Impulse Responses (RIRs) for B-format recordings. This dataset in .mat format has been utilized for generating the reverberant speech mixtures for my recent work named "Exploiting Angular and Spectral Features for B-Format Speech Separation with Deep Neural Networks".

Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures

The thylakoid membrane is in a temperature-sensitive equilibrium that shifts repeatedly during the life cycle in response to ambient temperature or solar irradiance. Plants respond to seasonal temperature by changing their thylakoid lipid composition, while a more rapid mechanism for short-term heat exposure is required. The emission of the small organic molecule isoprene has been postulated as one such possible rapid mechanism. The protective mechanism of isoprene is not known, but some plants emit isoprene during periods of high-temperature stress. In this work, we investigate the dynamics and structure for lipids within a thylakoid membrane at different temperatures and varied isoprene content using classical molecular dynamics simulations. The results are compared with experimental findings from across the literature for temperature-dependent changes in the lipid composition and shape of thylakoids. We find that the surface area, volume, and flexibility of the membrane, as well as the lipid diffusion, increase with temperature, while the membrane thickness decreases. Saturated thylakoid 34:3 glycolipids derived from eukaryotic synthesis pathways exhibit significantly different dynamics than lipids from prokaryotic synthesis paths, which could explain the upregulation of specific lipid synthesis pathways at different temperatures. Increasing isoprene concentration was not observed to have a significant thermoprotective effect on the thylakoid membranes.

Raw GBIF data used in the article "Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles"

This table contains the raw (unfiltered) species occurrence data for Dianthus sylvestris complied from GBIF. A filtered subset of this data was combined with other data sources to define the input for the species distribution models used in the article "Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles".

opencc-zeroFeb 2023View details →

Functional traits of soil nematodes define their response to nitrogen fertilization

1. Nitrogen (N) fertilization and warming are two crucial global change factors affecting the soil nematode communities. The effects of N fertilization and warming, however, on nematode communities in soils are inconsistent across ecosystems and maybe be even opposite. 2. One key reason is that the commonly used taxonomic diversity is less sensitive to environmental changes than the seldom-used trait-based indicators. To verify this, we performed an eight-year field experiment with four N fertilization levels with and without soil warming and collected an extensive dataset consisting of (i) six traits related to the nematode performance, i.e., body size, maximum body length, maximum body width, stylet length, esophagus length, and intestinal length; (ii) the taxonomic alpha (richness and abundance) and beta-diversity (Bray-Curtis dissimilarities) of the whole nematode community and each nematode functional group, (iii) soil food web resources (the total taxonomic richness and abundance of plant, bacterial and fungal communities), and (iv) soil properties (pH, total, ammonium and nitrate N, microbial N and C, total and available P and soil water content). 3. We found that N fertilization altered plant diversity and soil nitrate levels, which in turn decreased taxonomic alpha diversity of two nematode functional groups (phytophagous nematodes and predators), but taxonomic diversity for the whole nematode community remained stable. The decreased taxonomic alpha diversity of phytophagous nematodes resulted in increased maximum body width, but decreased stylet length and esophageal length. Mild warming (~ 0.7 °C) had no effects on soil properties and soil food web resources, and the taxonomic diversity or nematode traits remained unchanged. 4. Our results reveal that nematode functional traits show strong responses to N fertilization as individual nematode groups adapted quickly to changed soil properties and food web resources. Taxonomic diversity indices, however, were more stable under these changes showing that the functional composition of nematode communities may respond in the short-term despite little effects on species diversity. Thus, the trait-based indicators not only reveal how nematodes respond to N fertilization, but also how nematodes mediate the effects of N fertilization on ecosystem functioning (i.e., soil nutrient cycling).

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Analysis of the Specific Immune Response after the Third Dose of mRNA COVID-19 Vaccines in Organ Transplant Recipients: Possible Spike-S1 Reactive IgA Signature in Protection from SARS-CoV-2 Infection

Background: Several studies have indicated that anti-SARS-CoV-2 mRNA vaccinations are less effective in inducing robust immune responses among solid organ transplant recipients (SOTRs) compared with the immunocompetent. The third dose of vaccine in SOTRs showed promising results of immunogenicity, even though clinical studies have suggested that immunocompromised subjects are less likely to build a protective immune response against SARS-CoV-2 resulting in lower vaccine efficacy for the prevention of severe COVID-19. Methods: Serological IgG and IgA were analyzed through CLIA or ELISA, respectively, while Spike-specific T cells were detected by ELISpot assay after the second and third dose of vaccine in 43 SOTRs. Results: The third dose induced an improvement in antibody response against SARS-CoV-2. We also reported a strong correlation between specific humoral and cellular responses after the third dose, even though we did not see significant changes in the magnitude of the SARS-CoV-2-specific T cell response. SOTRs who contracted the SARS-CoV-2 infection after the third dose, despite eliciting a positive IgG response, failed to mount an anti-Spike-S1 IgA response, both after the third dose and after SARS-CoV-2 infection. Conclusions: We can conclude that serum IgA detection can be helpful, along with IgG detection, for the evaluation of vaccine efficacy, principally in fragile subjects at high risk of infection.

opencc-by-4.0Mar 2023View details →

Contrasting Responses of Surface Heat Fluxes to Tropical Deforestation

2D_GSWP3*.nc are the CLM simulation outputs with GSWP3 as input forcings. 2D_*_piControl.nc and 2D_*_deforest-globe.nc are the CMIP6 model outputs. Offline.m and LUMIP.m are matlab code files to reproduce figures in the article. nc_*.py are python code files to generate netCDF files for producing figures.

opencc-zeroFeb 2023View details →

Navigating agricultural landscapes: Responses of critically endangered giant tortoises to farmland vegetation and infrastructure

Context: Interactions between wildlife and anthropogenic infrastructure, such as roads, fences, and dams, can influence wildlife movement, and potentially cause human-wildlife conflict. In the Galapagos archipelago, two species of critically endangered giant tortoise encounter infrastructure and human-modified vegetation in farms, which could influence movement choices. Objectives: We investigated factors influencing tortoise movement and habitat selection in the agricultural landscape of Santa Cruz Island, Galapagos. Methods: We examined the movement of 27 tortoises collected using GPS tracking between 2014 and 2020, in relation to the location of vegetation, ponds, fences, and roads. Results: We found that tortoises preferred pasture over native vegetation, but there was little difference among their preferences for native vegetation, crops, or invasive vegetation. Tortoises also travelled slower in pasture, and faster in invasive vegetation, compared to crops and native vegetation. Tortoises were more likely to be found closer to ponds than predicted by chance. Our results indicated that most fences were porous to tortoises, with limited impact on their movement. Tortoises were more likely to use areas near roads with low-traffic. Conclusions: Pastures and ponds are important habitats for tortoises in farms and are likely to be used preferentially by tortoises. Overall, fences and roads did not strongly obstruct tortoise movements, however, this may lead to potential injury to tortoises on roads and property damage for farmers. To best identify priority areas for managing wildlife on farms, we recommend evaluating the combined effects of multiple anthropogenic landscape features on wildlife movements.

opencc-zeroDec 2021View details →

Data for: Mercury contamination challenges the behavioral response of a keystone species to Arctic climate change

Combined effects of multiple, climate change-associated stressors are of mounting concern, especially in Arctic ecosystems. Elevated mercury (Hg) exposure in Arctic animals could affect behavioural responses to changes in foraging landscapes linked to climate change, generating interactive effects on behaviour and population resilience. We investigated this hypothesis in the little auk (Alle alle), a keystone Arctic seabird. We compiled behavioural data using accelerometers, and quantified blood mercury and environmental conditions (sea surface temperature (SST), sea ice coverage (SIC)) across multiple years. Warm SST and low SIC reshaped time activity budgets (TABs) and diving patterns, causing decreased resting, increased flight, and longer dives. Mercury contamination was not associated with TABs. However, highly contaminated birds lengthened inter-dive breaks when making long dives, suggesting mercury-induced physiological limitations. As dive durations increased with warm SST, subtle toxicological effects threaten to increasingly constrain diving and foraging efficiency as climate change progresses, with ecosystem-wide repercussions.

opencc-by-4.0Feb 2023View details →

Stomatal response data for Pleopeltis polypodioides

Spreadsheet that contains stomatal responses of Pleopeltis polypodioides leaves to physiological treatments and abscisic acid.