Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
104
datasets available to search
ShareScore release 0.9.0
Dataset results
104 results for “heterotrophs”
Dataset for the paper submitted for peer-review with the title "Quantifying heterotrophic bacteria parameters and dissolved organic carbon biodegradability through oxygen data assimilation in a river water quality model"
<p>The proposed dataset is related to the following article submitted for peer review:</p> <p>Hasanyar, M., Flipo, N., Romary, T., Wang, S. (2023), Quantifying heterotrophic bacteria parameters and dissolved organic carbon biodegradability through oxygen data assimilation in a river water quality model, UNDER PEER-REVIEW</p> <p>It consists of command files for the prose-pa0.74 software available here: https://gitlab.com/prose-pa/prose-pa </p> <p>To run the model :</p> <p>1. Compile prose-pa0.74</p> <p>2. Copy the executable in the current directory</p> <p>3. In a terminal launch</p> <p>> ./prose-pa0.74 simulation.COMM test.log</p> <p>The “simulation.COMM” holds the settings for the ProSe-PA simulation related to the paper mentioned in the front head of the current file. </p> <p>The information on different parameters of “simulation.COMM” are included in “bathymetrie”, “Cmds”, “Inflows”, “layers”, “meteo”, “o2_obs”, “param_bio”, “Reaches” and “Singularities” folders.</p> <p>The “bathymetrie” folder holds the geometric information of several cross-sections along the river. </p> <p>The Cmds folder holds the “simulation.COMM” file. </p> <p>The “Inflows” folder the information about the boundary condition inflows to the river such as discharge, concentration of organic carbon, etc.</p> <p>The layer folder holds data of the initial conditions of the model (Table 2 in the article).</p> <p>The “meteo” folder holds the meteorological information.</p> <p>The “o2_obs” folder holds the observed oxygen data needed to do data assimilation. </p> <p>The “param_bio” folder holds information on the physiology of bacteria, phytoplankton, and other model species.</p> <p>The “Reaches” folder holds information about river reaches and their manning coefficient. </p> <p>The “param_range” file holds the variation range of model parameters considered in data assimilation together with their perturbation percentage.</p> <p>The output files are written in $HOME/Outputs folder. It is possible to change it directly in simulation.COMM, last entry “Output_folder”.</p>
Dataset and codes for: Partitioning the apparent temperature sensitivity between autotrophic and heterotrophic protists
Open the record for dataset details and reuse information.
Changes in vegetation in northern Alaska under scenarios of climate change, 2003-2100: III - Decadal net primary productivity (NPP) and heterotrophic respiration
These data contain NPP, NEP, and RH values from northern AK based on a modeling study for the years 2003-2100. See Euskirchen et al., 2009 for more information. V This file contains data for Figure 5.
Algae alleviate carbon limitation of heterotrophic bacteria in a boreal peatland
In most high latitude wetlands, carbon accumulation as peat represents a balance between plant net primary productivity and heterotrophic decomposition. We hypothesized that this assessment of ecosystem metabolism is incomplete as it does not include information on energy inputs from microalgae, which form complex biofilms with heterotrophic microorganisms on the peat surface. To investigate the potential for algae (and associated exudates) to support heterotrophic metabolism under ambient and elevated nutrient levels, we conducted a factorial enrichment of nutrients (nitrogen and phosphorus) and carbon (glucose) in mesocosms with and without the presence of algae (using light-transparent and dark treatments, respectively) in an Alaskan fen. We measured respiration rates and changes in bacterial biomass to characterize the response of heterotrophic bacteria to our experimental treatments. During incubation assays, algae released up to 38% of their net productivity as exudates and there was a positive relationship between algal production and concentrations of dissolved organic carbon inside mesocosms. Elevated algal productivity in the presence of nutrient enrichment stimulated heterotrophic bacterial respiration and biomass. These responses did not occur with nutrient enrichment in the dark (without algae). The response of bacteria to algae was similar in magnitude to bacterial responses to glucose enrichment. We conclude that bacteria in this boreal fen were primarily limited by labile carbon and this constraint was alleviated in the presence of elevated algal production. Consequently, algae may facilitate hotspots of microbial activity in northern peatlands, especially in conditions of greater nutrient availability associated with more variable hydrology expected for this region with ongoing climate change.
McMurdo Dry Valleys Microzooplankton : Cryptophyte, Ciliate, and Heterotrophic Nanoflagellate Abundances
In conjunction with the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, lakes were monitored for microzooplankton by a team based out of the University of Nottingham (led by Johanna Laybourn-Parry). This dataset shows the abundance of heterotrophic nanoflagellates, cryptophytes, and ciliates found at various depths in Lake Fryxell and Lake Hoare.
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Data from: Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs
<p>Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly-studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes (SAGs), and only a single formal described species, <em>Eupelagonema oceanica</em>. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows these two cells represent distinct subclades within eupelagonemids, each different from <em>E. oceanica</em>. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data, and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.</p>
Functioning of a canopy-dominated intertidal community during emersion: highly productive but heterotrophic at the annual scale - R code
<p>This repository contains the data and code for our paper:</p> <p>Claire Golléty, Jon Yearsley, Aline Migné, Dominique Davoult (2024). Functioning of a canopy-dominated intertidal community during emersion: highly productive but heterotrophic at the annual scale. Marine Biology<br>https://doi.org/10.1007/s00227-024-04395-5</p>
Fig. 1 in Free-living Heterotrophic Flagellates Lakes in Turkey (Protista) from Two Hypersaline
Fig. 1. Map of study sites.
Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution
<p>Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.</p>
Data from: Competition between mixo- and heterotrophic ciliates under dynamic resource supply
<p>The outcome of species competition strongly depends on the traits of the competitors and associated trade-offs, as well as on environmental variability. Here we investigate the relevance of consumer trait variation for species coexistence in a ciliate consumer – microalgal prey system under fluctuating regimes of resource supply. We focus on consumer competition and feeding traits, and specifically on the consumer's ability to overcome periods of resource limitation by mixotrophy, i. e. the ability of photosynthetic carbon fixation via algal symbionts in addition to phagotrophy. In a 48-day chemostat experiment, we investigated competitive interactions of different heterotrophic and mixotrophic ciliates of the genera <em>Euplotes</em> and <em>Coleps</em> under different resource regimes, providing prey either continuously or in pulses under constant or fluctuating light, entailing periods of resource depletion in fluctuating environments, but overall providing the same amount of prey and light. Although ultimate competition results remained unaffected, population dynamics of mixotrophic and heterotrophic ciliates were significantly altered by resource supply mode. However, the effects differed among species combinations and changed over time. Whether mixotrophs or heterotrophs dominated in competition strongly depended on the genera of the competing species and thus species-specific differences in the minimum resource requirements that are associated with feeding on shared prey, nutrient uptake, light harvesting and access to additional resources such as bacteria. Potential differences in the curvature of the species' resource-dependent growth functions may have further mediated the species-specific responses to the different resource supply modes. Overall, our study demonstrates that genus- or species-specific traits other than related to nutritional mode may override the relevance of acquired phototrophy by heterotrophs in competitive interactions, and that the potential advantage of photosynthetic carbon fixation of symbiont-bearing mixotrophs in competition with pure heterotrophs may differ greatly among different mixotrophs, playing out under different environmental conditions and depending on the specific requirements of the species. Complex trophic interactions determine the outcome of competition, which can only be understood by taking on a multidimensional trait perspective.</p>
Fig. 4 in The Robin, Erithacus Rubecula (Passeriformes, Turdidae), As A Component Of Heterotrophic Consortia Of Forest Cenoses, Northeast Ukraine. Part 2
Fig. 4. Direct consortial relations of robins.
Data from: Phosphorus limitation determines the quality of dissolved organic matter released by marine heterotrophic prokaryotes
<p>We determined phosphorus (P) limitation effect on the quantity and quality of dissolved organic matter (DOM) released by heterotrophic prokaryotes (HP). We grew 2 single bacterial strains, Photobacterium angustum and Sphingopyxis alaskensis, and natural HP communities collected in fall and spring from the Mediterranean Sea, on glucose under 2 treatments: P-replete vs. P-limiting. DOM release by HP comprised up to 30 % of the initial carbon provided for growth. P availability influenced carbon allocation to different cellular processes (respiration vs. growth), but did not significantly affect the quantity of DOM released by HP. However, using fluorescence spectroscopy, we demonstrated an effect of P-limitation on DOM quality, with a predominance of humic-like compounds under P-limitation but protein-like compounds under P-repletion. Our results suggest that P-limitation could determine the fate of HP-derived DOM in the ocean, thus affecting the microbial carbon pump.</p>
Data for: Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates
<p><span>The function of the eye-like ocelloid in warnowiid dinoflagellates remains unknown because warnowiids are rare and uncultured, and scant molecular data exists for this group. While the ocelloid resembles the camera-type eyes found in animals, it is composed of organelles, with a highly modified plastid serving as the retinal body. By performing single-cell transcriptomics on cells isolated from the environment, we generate a comprehensive molecular dataset of warnowiids that includes all four known genera and one previously undescribed genus. We show that the heterotrophic members of this group have retained and express components of the ancestral photosynthetic mechanism, seemingly without photosystem II and RuBisCo. Our findings suggest that the ocelloid retinal body has repurposed the remaining photosystem to perform a function other than photosynthesis.</span></p>
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Open the record for dataset details and reuse information.
Data from: Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs
Open the record for dataset details and reuse information.
Data for: Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates
Open the record for dataset details and reuse information.
Data from: Competition between mixo- and heterotrophic ciliates under dynamic resource supply
Open the record for dataset details and reuse information.
Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution
Open the record for dataset details and reuse information.
Data from: Phosphorus limitation determines the quality of dissolved organic matter released by marine heterotrophic prokaryotes
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.