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opencc-zeroMar 2023View details →

Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

The data in this archive are the results of a study on the impact of heavy metals (HMs) on the soil microbiota of an urban Superfund site in Alabama. HMs are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease.

publicJul 2025View details →

Metadata from: Rhizosphere bacteria and fungi are differentially structured by host plants, soil mineralogy and ectomycorrhizal communities in the Alaskan tundra

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publicFeb 2021View details →

Use of Deep Learning for structural analysis of CT-images of soil samples

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publicMar 2023View details →

Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

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publicJun 2022View details →

Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

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opencc-zeroDec 2019View details →

Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression

1. Plant-derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, most data are case-specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots – sugars, amino acids, organic acids and phenolic acids – can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression. 2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil-borne Ralstonia solanacearum bacterial pathogen. 3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen-containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity. 4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.

opencc-zeroJan 2020View details →

Effects of past and present-day landscape structure on forest soil microorganisms

Principles of landscape ecology have been built on birds and plant species distribution, but the number of clues is now growing on below-ground organisms, whose dispersal may also be affected by above-ground landscape structure. For communities of microorganisms, the question remains if and how they answer to landscape structure, with or without time lag, and if some groups of microorganisms may react more than others. Here, we investigated if fungi or bacteria diversity is driven by the amount of forest cover in the current or the past landscape. We tested the Habitat Amount Hypothesis (HAH) on ancient forests of Cevennes national park, that were particularly fragmented 150 years ago, and are today surrounded by recent forests. As ancient forests are often more diverse in plant species, we hypothesized that the higher quantity of ancient forests in the landscape, the richer fungal and bacterial communities would be locally. More precisely, we expected that ectomycorrhizal fungi, and pathotrophic fungi, often indicators of mature forests, would be also more sensitive to forest history and therefore to the quantity of ancient forests than bacteria and saprotrophic fungi. We sampled 40 soil cores per 0.5 ha, pooled in 8 composite samples per plot in 27 landscapes and sequenced ITS and 16S marker by Illumina-Mi seq. To identify functional groups of fungi, we relied on their taxonomy and the use of public databases. Our results partly follow the HAH, as fungi richness was positively related with the quantity of ancient forests in the landscape and not by the focal patch size. Ectomycorrhizal and pathotrophic fungi were positively affected by the ancient forest cover, and so were saprotrophic ones, but not bacteria. Local factors also shaped the communities such as soil composition and elevation, confirming classical patterns in soil ecology. Interestingly, past landscape structure better explained fungi communities richness than contemporary landscape, suggesting a time lag in the response of communities to landscape modification and a potential extinction debt. Our results invite to consider below-ground communities in landscape studies and historical ecology, as their structure and functions might be intimately linked with soil and landscape history.

opencc-by-4.0Oct 2022View details →

Cover crops improve soil structure and change OC distribution in aggregate fractions

Data set and R script on the statistic evaluation of soil data. The data derived from a long-term field trial at the Asendorf field station 70 km north of Hanover, Germany (49 m above sea level, 52°45′48.4′′N 9°01′24.3′′E). Data include soil data (OC, TN, bulk density, texture) as well as data from soil aggregate fractionation and evaluation of their aggregate stability.  All methods and data will be described in an upcoming journal article (DOI will be provided soon).

opencc-zeroMay 2022View details →

Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however, preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial spatial association of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that changes in AM fungal proportional abundance induced by spatial structure in roots of a preferentially allocating host produced positive feedbacks on plant growth, showing that interactions between spatial structure and host choice can determine the direction of plant-soil feedbacks. Our results suggest that symbiont spatial structure within plant roots may act as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with potentially cascading effects on plant-plant interactions.

opencc-zeroJun 2022View details →

Trophic structure and origin of resources of soil macrofauna in the salt marsh of the Wadden Sea: a stable isotope (15N,13C) study

Salt marshes exist along the gradient of the marine mudflat to the terrestrial dunes, with a gradient of shore height and associated plant zonation. The lower salt marsh (LSM) extends from the mean high tidal level to 35 cm above that level and is followed by the upper salt marsh (USM). Despite changes in the amount of allochthonous marine input and in abiotic conditions, little is known about changes in the trophic structure and used of basal resources by the soil macrofauna along marine – terrestrial boundaries. Natural variations in carbon stable isotope ratios (δ¹³C signatures) allow insight into basal resources of consumers such as marine algae, terrestrial C3 and C4 photosynthesising plants. Furthermore, variations in nitrogen stable isotope ratios (δ¹5N signatures) allow insight into the trophic position of consumers. We investigated spatial and temporal changes in stable isotope signatures in salt marsh soil macrofauna of the island of Spiekeroog, German Wadden Sea. The range of δ¹⁵N signatures indicated no changes in food chain length across salt marsh zones with consumers in both zones comprising primary decomposer, secondary decomposer and first order predators. However, the trophic position of individual species changed between zones, but in particular with season. Contrasting δ¹⁵N signatures, the range in δ¹³C signatures in the LSM was twice that in the USM indicating a wider range of resources consumed. Bayesian mixing models indicated predominant autochthonous resource use in both the LSM and USM, with the use of marine allochthonous resources never exceeding 29.6%. However, the models also indicate an increase in the use of marine resources in certain species in the LSM with no use in the USM. Overall, the results indicate that the resource use of salt marsh macrofauna varies more in space than in time, with the food web being generally based on autochthonous rather than allochthonous resources. However, there also is trophic plasticity in certain species across both temporal and spatial scales including variations in the use of allochthonous resources. Generally, however, marine input contributes little to the nutrition of salt marsh soil macroinvertebrates.

embargoedcc-by-4.0Dec 2021View details →

Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project

Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.

opencc-zeroAug 2022View details →

Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure

Biochar can significantly change soil properties and improve soil quality. However, the effects of long-term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure and crop yield are still obscure. We characterized these relationships in a long-term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha-1 year-1 (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha-1 year-1 (N0 and N). The repeated, long-term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon and nitrogen (MBC and MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as the amount of total phospholipid fatty acids. The activity of leucine aminopeptidase (LAP) decreased significantly in the biochar-amended and N fertilized treatment, but the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum Chloroflexi was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α-1,4-xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN and LAP activity. In addition, long-term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long-term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.

opencc-by-4.0Oct 2018View details →

Geophysical data from: "A review of geophysical methods for soil structure characterization"

The geophysical data presented herein was collected in the Soil Structure Observatory (see, Keller et. al. 2017) and were used to create Figures 4b, 5a, 5b, 9a and 9b for the manuscript entitled: "A review of geophysical methods for soil structure characterization" submitted to reviews of geophysics. The data set includes: GPR data collected from South to North in the bare soil of block C before and after compaction GPR_800Mhz_BSbeforecompaction.DZW GPR_800Mhz_BSbeforecompaction.DZT GPR_800Mhz_BSaftercompaction.DZW GPR_800Mhz_BSaftercompaction.DZT ERT data collected from South to North in the bare soil of block B before and after compaction ERT_B2_14-03beforecompaction.bin ERT_B2_14-04aftercompaction.bin Time-lapse ERT data collected in block A in September of 2017: timelapseERT2017.zip The date and time in the files names indicate the time in which the resistivimeter started collecting data plus two hours. e.g. for 2017-09-11-18-01-41.bin, the first data point was collected at 14:01 on the 11th of September of 2017. The first 464 data points correspond to bare soil collected from North to South The following 464 data points correspond to grassy soil from South to North Meteorological data from 2017 meteodata_Reckenholz2017.xls Time domain reflectometry data from September of 2017 for block A (10, 20, 40 and 70cm depth). Two land covers (bare soil and grassy soil) and two compaction treatments (full compacted and non compacted) are included. TDR_A1_Sept2017.xlsx   Keller, T., Colombi, T., Ruiz, S., Manalili, M. P., Rek, J., Stadelmann, V., ... & Schymanski, S. (2017). Long-Term Soil Structure Observatory for Monitoring Post-Compaction Evolution of Soil Structure. Vadose Zone Journal, 16(4).

opencc-by-4.0May 2019View details →

Figure 5 in Structural characteristics of the soil fauna community in beach wetlands of the Poyang Lake region

Figure 5. Margalef index (D) of soil fauna community at different sampling sites.

opencc-zeroJun 2023View details →

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

opencc-by-4.0Jul 2023View details →

Supplementary material/Organic carbon dynamics in clay soils: impact of management practices on microorganism structure and abundance under semi-arid conditions

Proper management of soil organic matter in arid and semi-arid regions improves organic carbon storage in the soil, helps in compact soil degradation, and mitigates climate change impacts, and preserves ecosystem functionality and sustainability food security. This study aims to provide a better insight into the biogeochemical processes that drive the organic carbon dynamics of saline clay soil in a semi-arid climate. The study is not intended to be exhaustive but contributes to analyzing the relationship between bacterial microflora, physicochemical properties, and organic carbon dynamics as a function of different soil management modes. The monitoring was carried out on three different plots located at the National Institute of Agronomic Research of Algeria. A physicochemical characterization of the soils was performed. A metagenomic study was also conducted to identify bacterial biodiversity using PCR-amplified DNA sequencing. The study results show that the control plot has the highest average organic carbon stock value at 47 Mg ha-1. This was followed by the amended plot and the conventional plot, respectively, with 43 Mg ha-1 and 38 Mg ha-1. In the context of this study, organic carbon dynamics would appear to depend on the interaction of several biotic and abiotic factors. Soil management methods would impact the density and diversity of bacterial microflora. This, in turn, affects the soil's physicochemical properties and, more specifically, organic carbon dynamics and storage.

publicApr 2020View details →

Data from: Soil biotic quality lacks spatial structure and is positively associated with fertility in a northern grassland

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publicOct 2025View details →

Data from: Herbivore species and patch heterogeneity modulate grazing-induced shifts in soil nematode trophic structure and energy flux

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