cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17041496.v1
title: Data for Locomotor activity patterns of wild Natal mole-rats suggest entrainment of circadian activity to burrow temperatures

description: We utilized an RFID reader array (LID650/608, DorsetID, The Netherlands) to monitor mole-rat activity during winter (August - October 2020) and summer (February - April 2021). Mole-rats wree implanted with a subcutaneous transponder and released into their burrow. Animals were weighed, sexed, and assigned a reproductive class upon capture. The array was programed to scan continuously for transponder tags within range with a read delay of 3 seconds and save transponder codes with a time stamp. Thus, if an animal remained in the range of the panel for longer than 3 seconds, it would have multiple entries at 3-second intervals. The reader would then store the transponder code and the date and time. We assumed activity bouts lasted for 1 hour and animals were given an active score of 1 if a reading was detected on the array during a 60-minute period, and a score of 0 if not detected. An animal would not gain a further activity point until detected beyond the activity period. Individuals captured in the group but not recorded by the RFID reader array were assigned activity scores of zero.<br>Hourly air pressure, air temperature, soil temperature, and rainfall for winter 2020 and summer 2021 were obtained from the global atmospheric reanalysis dataset ERA5-Land which is freely available from the Copernicus Climate Change Service, which holds the intellectual property rights of the raw climate data. The results contain modified Copernicus Climate Change Service information. Soil temperatures in the dataset correspond to the depths of foraging tunnels and the nest of mole-rats. The change in hourly air pressure (ΔP) from hour 1 to hour 2 was calculated to determine whether changes in air pressure predicted activity. These data were then combined with the activity data to determine the environmental effects of daily and seasonal activity patterns.<br>
DOI: 10.6084/m9.figshare.16985323.v2
title: Saved Objects

description: Cropped tumour region from CT scan images and saved trained models
DOI: 10.6084/m9.figshare.16985323
title: Saved Objects

description: Cropped tumour region from CT scan images and saved trained models
DOI: 10.6084/m9.figshare.16985323.v4
title: Saved Objects

description: Cropped tumour region from CT scan images and saved trained models
DOI: 10.6084/m9.figshare.16985323.v3
title: Saved Objects

description: Cropped tumour region from CT scan images and saved trained models
DOI: 10.6084/m9.figshare.17938085.v1
title: Lyster et al. - Hydraulic geometries of natural rivers

description: A dataset of hydraulic geometries in natural rivers. See the sheet entitled "readme" for information on the contents of this dataset. This dataset is supplementary material for a manuscript that is currently in review for publication.
DOI: 10.6084/m9.figshare.17938085
title: Lyster et al. - Hydraulic geometries of natural rivers

description: A dataset of hydraulic geometries in natural rivers. See the sheet entitled "readme" for information on the contents of this dataset. This dataset is supplementary material for a manuscript that is currently in review for publication.
DOI: 10.6084/m9.figshare.16586324
title: scrap file

description: KEGG pathway enrichment for H-VAE-Cox model and X-VAE-Cox model
DOI: 10.6084/m9.figshare.16586324.v2
title: scrap file

description: KEGG pathway enrichment for H-VAE-Cox model and X-VAE-Cox model
DOI: 10.6084/m9.figshare.16586324.v1
title: KEGG-Pathway.xlsx

description: KEGG pathway enrichment for H-VAE-Cox model and X-VAE-Cox model
DOI: 10.20387/bonares-eyt4-dc84
title: Earthworm data 2018 in agroforestry and monoculture - Bonares-SIGNAL-Projekt

description: Earthworm biomass was determined based on earthworm hand-sorting from a 0.25 x 0.25 x 0.25 m soil block in summer 2018. All earthworms were collected from the soil, stored on filterpaper for 24h. The earthworms were than weighted after the guts were empty. Earthworm biomass is given as the sum of all earthworms from one soil block related to a surface area of 1m2.

Research domain: Soil Sciences
DOI: 10.20387/bonares-t355-h550
title: Corn and straw yields at the agroforestry site Forst, Brandenburg starting 2019

description: Barley (Hordeum vulgare) and bristle oat (Avena strigosa) were harvested at the agroforestry site in Forst and the reference site on July 25th, 2019, and July, 30th 2020, respectively. After plots were harvested using a plot combine harvester subsamples were oven dried for 24 hrs at 105°C to determine water content and dry weights of the samples. The table contains the fresh weights of the harvested barley and bristle oat corn and straw biomass, the weights of the subsamples before and after oven-drying, the weight of the containers used for oven drying as well as the corn and straw dry weight yields in t/ha calculated from these parameters.

Research question: Does crop productivity differ at agroforestry sites vs. treeless reference sites?
Within the agroforestry site, are crop yields different at different distances to the tree rows?
DOI: 10.20387/bonares-2rn4-s965
title: Pictures for 'Regional climate change observational data FOR 1695'

description: The pictures can be downloaded here:
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC1.zip
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC2.zip
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC3.zip
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC4.zip
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC5.zip
https://metadata.bonares.de/smartEditor/rest/upload/08_GVF_EC6.zip

EC 1-6 corresponds to the eddy covariance stations at the research sites 1-6, respectively.

The corresponding publication can be accessed here: https://doi.org/10.5194/essd-2020-396

Dataset version 1.0
DOI: 10.20387/bonares-x13m-z796
title: Gross N2O emission and uptake in cropland agroforestry and monoculture systems

description: This data set includes data on gross N2O emission and uptake measured by 15N2O pool dilution, net N2O flux, CO2 emission, soil temperature, water-filled pore space, mineral N (NH4+ and NO3-), microbial biomass N and C, and denitrification gene abundance (nirK, nirS, nosZ clade I and II) were measured on three sites in Germany in cropland agroforestry and monocultures. Each site is represented by 4 replicates per land use, at the following distances from the tree row for agroforestry: 1m, 7m and 24m.

Research domain: Soil Sciences

Research question:
Does agroforestry reduce gross N2O emission from the soil and increase gross N2O uptake from the atmosphere into the soil compared to monoculture system?
DOI: 10.20387/bonares-vcr5-zb43
title: DiControl Soil GPS Data Set (Data collection)

description: We conducted a minirhizotron experiment with soil samples taken in 2016 from the field sites of three long-term experiments, belonging to the Humboldt- Universität zu Berlin (HUB; Thyrow) and the Research Institute of Organic Agriculture (FIBL; Therwil) and the LTE in Bernburg (Anhalt-University). The soil, which underwent different fertilization strategies (mineral vs. organic and biodynamic fertilization vs. reduced and full N-fertilization) and cultivation practices (plough vs. cultivator) was used to cultivate lettuce as model plant in minirhizotrons for 9 weeks and 6 weeks under controlled growth chamber experiments at the IGZ-Großbeeren and the University of Hohenheim.

Research domain: Plant Cultivation and Agricultural Technology

Research question: The experiment was established to study the different effects of fertilization management and soil cultivation on the yet unknown interactions of rhizodeposits and rhizosphere chemistry with its associated rhizosphere soil microbiota (fungal, bacterial and archaeal communities) and their impact on plant health and stress resilience in lettuce. 

For further information’s see Windisch et al. 2021, frontiers in Microbiology, doi: 10.3389/fmicb.2020.597745

The experiment was designed to investigate the differential effects of fertilizer management and tillage on the previously unknown interactions of rhizodeposites and rhizosphere chemistry with the associated rhizospheric soil microbiota (fungal, bacterial, and archaeal communities) and their influence on plant health and stress resistance in lettuce. The microbial community data collected are stored in the NCBI database and are accessible to everyone.
DOI: 10.20387/bonares-mpzr-ja21
title: Dataset of indicators for the assessment of soil-management related ecosystem services

description: We conducted a review of journal articles to identify suitable indicators for measuring the supply of ecosystem services in the context of agricultural land and soil management. A keyword-based search was conducted in Web of Science Core Collection and SCOPUS, using the terms “ecosystems service” AND “indicator” AND “agricultur*”. The search was restricted to articles in English published between January 2014 and January 2019. We identified 227 articles, out of which 179 met our selection criteria. Using a full-text review, we extracted information on ecosystem services addressed and indicators used. We also recorded the type of input data used and the spatial scale the indicators were used at or recommended for. Where studies used ecosystem service definitions other than the Common International Classification of Ecosystem Services (CICES V.5.1), indicators were assigned to the corresponding CICES class or classes. We used the information derived from the review to create factsheets for 37 ecosystem services relevant to agricultural land and soil management. Each factsheet provides tables with available indicators applicable at spatial scales ranging from field to global, information on the type of input data required and a link to the complete bibliographic information of the article or articles the indicator was taken from. Since the dataset is based on a systematic sample of publications on ecosystem service supply, it indicates the current research focus and research gaps. The dataset provides an indicator toolbox that researchers can use to find the indicators best suited to their research needs.
DOI: 10.20387/bonares-9wg3-tme7
title: Soil management-related stakeholder database in German agricultural sector

description: In order to support sustainable soil management, an exchange between scientists and other soil-related stakeholders is crucial. Hence, an overview on soil-related stakeholders in Germany is required and was prepared in the form of dataset. The five listed-below stakeholder groups, which were assumed to have a direct or indirect influence on soil functions, were initially derived from the drivers of soil management (i.e. socio‐economic, biophysical, and technology). The groups were defined such as (1) state authorities, (2) civil societies, (3) land owners and land owner associations, (4) agricultural associations and (5) soil management-related enterprises. The stakeholders’ influence/power and interest were evaluated with the focus of organizations on the five main soil functions, i.e. production, water purification, carbon sequestration, biodiversity, recycling of nutrients and chemicals. 
The level of the influence/power and interest was estimated in a relative matter among the stakeholders by taking into account such parameters as the number of members/partners/employees, the visibility of projects/products/policies/press/publications etc. as well as the hierarchy among the state organizations. While the size of the privatized land area and its use were of the utmost importance for the land owners. In addition, the level of awareness of stakeholders’ activities played a role in assessing the stakeholders’ influence.

Research domain: Soil Sciences

Research question: The aim was to create a stakeholder database, representing soil-related stakeholders across Germany at the national scale.
DOI: 10.20387/bonares-9bbk-z07e
title: Terrestrial and Aquatic Kraatz and Rittgarten Kettle Hole Experiments (ID)

description: This is a data set collection of kettle hole studies in the frame of the SAW project "LandScales". 
This ID-table defines all measurement types, positions, dates and/or depths (=mother table).

Research domain: Soil Sciences

Research question: Small inland water bodies are known to be dominated by terrigenous material; however, the processes and structures that drive the enrichment and depletion of specific geochemical elements in the sediment and water column remain unclear. It is hypothesized that the mobile elements (Ca, Fe, K, P) behave different from each other in their transport, intermediate soil retention, and final accumulation in the water body’s sediment.

These data accompanying analyses and interpretations of the paper Nitzsche et al. "Glacial kettle holes reflect the biogeochemical characteristics of their catchment area and the intensity of the element-specific input".
DOI: 10.20387/bonares-8fhj-r52g
title: Long-term field experiment V140 Muencheberg from (launched in 1963) - Plots

description: Parent table of long-term field experiment V140 Muencheberg. This data collection consists of 30 individual tables which are related to each other.

General description of the Long-term Field Experiment "V140": The long-term field experiment "V140" was established in 1963 at the experimental site of the present Leibniz Centre for Agricultural Landscape Research (ZALF) about 50 km east of Berlin in the district Märkisch-Oderland. The area is characterized by dry periods, particularly during early summer. The long-term average annual precipitation rate and tempeature is 536 mm and 8.8°C, respectively. Weather data for the running period of V140 are available at the DWD (station number 03376 via https://opendata.dwd.de/climate_environment/CDC/observations_germany/climate/daily/kl/historical/). The V140 represents one of the few still active long-term field experiments on sandy soil. During the running period just smaller management measures changes have been done. Whereas originally questions to yield increase measures on sandy soil were in focus, present research put more focus on the effects of organic and mineral fertilization on essential aspects of the soil fertility. The V140 is around 0.5 ha and is located on a flat area. Before the establishment of V140 the site was cultivated uniformly. According to the German Guidelines Soil Assessment (Bodenschätzung) the dominating soil types are slightly loamy sand and sand (Sl4D and S4D). The most common soil sub type is Haplic Luvisol. The experiment includes 21 treatments: 5 levels of mineral fertilization combined with 4 levels of organic fertilization and one control.

More information, e.g., database scheme, assorted literature overview, the detailed location plan, etc., can be found in the supplemental material.
DOI: 10.20387/bonares-k85p-tr5n
title: Survey of farmers on their perception of soil compaction and application of soil conservation measures

description: While the scientific aspects of soil compaction are studied since decades, there is hardly insight on knowledge and perception of this topic among farmers. Furthermore, there is hardly information on the dissemination of soil conservation measures to avoid soil compaction. For this reason, we conducted a German-wide online survey among farmers on this topic in autumn/winter 2017/2018. A further aim was to collect information on the dissemination of new technologies (apps) and to identify possible gaps in information services. The quantitative survey was conducted with the software LimeSurvey. Farmers were invited via various channels (professional journals, mailing lists of interest groups, Thünen homepage). The questionnaire contained the following thematic blocks: 1. general information on the farm, 2. soil compaction (perception and measures), 3. crop rotation and soil tillage, 4. technical equipment/process organisation (incl. contractors), 5. consulting and information offers (incl. apps). 

Research domain: Agricultural Economics and Sociology
DOI: 10.20387/bonares-sea4-n5sp
title: Arbuscular Mycorrhizal Fungal (AMF) Community During Crop Rotation, Lüneburg, Germany - OTU data

description: The dataset reports the contingency table of AMF sequence variants, their associated DNA sequence, accession number, and taxonomy. AMF come from soil or root samples from a two growing-season mesocosm experiment mimicking a crop rotation, with a first phase growing AM or non-AM and/or rhizobial or non rhizobial precrops followed with an AM crop. During the second phase, organic fertilization was applied (saw dust or wheat straw). The aim is to test the effect of precrop plant symbiotic functional group on following crop AM fungal diversity and abundance. Four crop plant species were used to have a combination of all symbiotic groups: spring canola (Brassica napus cv. Medicus, NPZ, non-rhizobial / non-AM), withe lupine (Lupinus albus cv. Energy, Feldsaaten Freudenberger, rhizobial / non-AM),  spring barley (Hordeum vulgare cv. Barke, Saatzucht Breun, non rhizobial/AM) faba bean (Vicia faba cv. Tiffany, NPZ, rhizobial / AM). The succeeding crop was winter barley (Hordeum vulgare, cv. Antonella, Nordsaat Saatzucht, non-rhizobial / AM). The AMF community structure was analyzed by amplicon sequencing of the D1-D2 region of the fungal LSU (28S) rRNA gene using the primers LR2rev (5'-GAAAAGAACTTTGAAAA-3') and LR3 (5'-CCGTGTTTCAAGACG-3'). The taxonomy and sequence for each sequence variant is included. The sequences were generated using the primers LR2rev (5'-GAAAAGAACTTTGAAAA-3') and LR3 (5'-CCGTGTTTCAAGACG-3'). The results revealed that the mycorrhizal precrop symbiotic group (AM or not AM), but not the rhizobial one (N2-fixer or not N2-fixer), affected the richness and composition of AM fungi in the soil. The effect on composition, but not on richness, persisted in the following crop, demonstrating a legacy effect of precrop functional group. However, this effect was weaker than that of contemporary factors such as nutrient addition. AMF community composition correlated to decreasing crop yield after AM precrops. Phylogenetic analyses revealed that differences in AMF communities pertained at deep phylogenetic levels. These findings suggest negative plant-soil feedbacks within the AM symbiosis in agro-ecosystems typical of western Europe, driven by the consistent selection of deep clades of AM fungi. The raw fastq read files are available under BioProject accession number ENA PRJEB36419. The sequence variant sequences are available at ENA under accession number LR761341-LR761569. Related publications: (1) van Duijnen, R., Roy, J., Härdtle, W., & Temperton, V. M. (2018). Precrop Functional Group Identity Affects Yield of Winter Barley but Less so High Carbon Amendments in a Mesocosm Experiment. Frontiers in Plant Science, 9, 1–12. doi: 10.3389/fpls.2018.00912. (2) Roy, J., van Duijnen, R., Leifheit, E., Mbedi S., Temperton, V. M & Rillig, M.C. (accepted) Legacy effects of pre-crop plant functional group on fungal root symbionts of barley; Ecological Application.

Research domain: Soil Sciences

Research question: Do precrop have a legacy effect on the root fungal symbionts of the next crop?
DOI: 10.20387/bonares-xnhz-xw6e
title: Arbuscular Mycorrhizal Fungal (AMF) Community During Crop Rotation, Lüneburg, Germany - Metadata

description: The dataset reports the associated metadata table of samples from a two growing-season mesocosm experiment mimicking a crop rotation, with a first phase growing AM or non-AM and/or rhizobial or non rhizobial precrops followed with an AM crop. A treatment of high carbon amendment was also applied. We used four plant species to have a combination of all symbiotic groups: spring canola (Brassica napus cv. Medicus, NPZ, non-rhizobial / non-AM), withe lupine (Lupinus albus cv. Energy, Feldsaaten Freudenberger, rhizobial / non-AM), spring barley (Hordeum vulgare cv. Barke, Saatzucht Breun, non rhizobial/AM) faba bean (Vicia faba cv. Tiffany, NPZ, rhizobial / AM). The amendment was no amendment, wheat straw or saw dust. The succeeding crop was winter barley (Hordeum vulgare, cv. Antonella, Nordsaat Saatzucht, non-rhizobial / AM). The table reports the timing phase of sampling (t0 = original soil used for the experiment, t1 = soil sample after the precrop growth and harvest, t2 = soil and root samples after the growth / harvest of the crop), the precrop identity, the high carbon amendment, whether samples are from roots or soil. The associated paper is : Legacy effects of pre-crop plant functional group on fungal root symbionts of barley; Ecological Application.

Research domain: Soil Sciences

Research question: Do precrops have a legacy effect on the root fungal symbiont of the next crop?
DOI: 10.20387/bonares-dykr-eh37
title: ARD Splitroot

description: Apple replant disease (ARD) is a threat to apple fruit and tree production worldwide caused by shifts in the soil microbiome. Chemical and physical measures of soil disinfection are the most employed countermeasures but inter-row plantings demonstrate that ARD is widely immobile in the soil, which causes the plant to face ARD affected and healthy soil simultaneously in the field. We simulated this situation in a split-root approach in two experiments using rhizoboxes, soil from the ORDIAmur ARD references sites Heidgraben and Ellerhoop and the apple rootstock M26. Root growth was monitored via the transparent front panel of the rhizoboxes and shoot growth was measured weekly. After two weeks, root systems from a subset of plants were sampled for expression analysis of ARD candidate genes. After eight weeks, masses of roots and shoots were recorded and contents of selected phenolic compounds were analyzed.
Root and shoot growth were severely reduced whenever both compartments of the rhizobox were filled with ARD soil in comparison to both compartments filled with disinfected ARD soil. Plants with only half of the root system growing in ARD soil showed a local reduction in root growth with an intermediate shoot growth. In ARD affected roots, the expression of the three ARD biomarker genes, biphenyl synthase 3, biphenyl 4-hydroxylase and ethylene-responsive transcription factor 1B-like, was locally induced after two weeks in comparison to disinfected ARD or control soil. Phenolic compound profiles in the roots showed a high variation between samples and soils. The total phenolic content as well as the contents of epicatechin and an unknown phenolic compound were locally increased in roots grown in ARD soil in comparison to disinfected ARD soil after eight weeks. Our results show how apple plants focus their molecular defense towards ARD locally in the roots. The local nature of ARD presents both challenges in the assessment of ARD severity in the field as for possible management strategies involving soil tillage.

Research domain: Plant Breeding

Research question: The objectives of this study were (i) to link the previously observed localized growth response to a local response of the selected genes and phenolic metabolites and (ii) identify the phenolic compounds that can be useful in unraveling ARD.