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opencc-zeroJul 2023View details →

Data from: Litter quality controls tradeoffs in soil carbon decomposition and replenishment in a subtropical forest

Species-rich forests can produce litter of varying carbon (C) and nitrogen (N) composition (i.e., quality), which can affect decomposition and play a central role in long-term soil organic carbon (SOC) accumulation. However, how differences in litter quality affect SOC decomposition and formation remains unclear over the full litter decomposition trajectory. We followed the in-situ complete decomposition of added 13C-labelled high- (low C:N) and low-quality (high C:N) leaf-litter and its effect on particulate (POM) and mineral-associated (MAOM) organic matter fractions over two years in a natural subtropical forest. We found that during early stages of decomposition, low-quality litter inputs decreased SOC via a positive priming effect (i.e., new C inputs favored decomposition of native SOC), but these SOC losses were offset by SOC gains observed via a negative priming effect during decomposition of high-quality litter. In contrast, this pattern reversed during late stages of decomposition—SOC losses via a positive priming effect induced by high-quality litter were offset by SOC gains via a negative priming effect induced by low-quality litter. Over the full decomposition of litter, both high- and low-quality litter stimulated microbial breakdown of SOC tied to POM, but also replenished more persistent SOC that associated with soil minerals (MAOM). Altogether, we observed that low-quality litter formed twice as much new SOC as high-quality litter (24% vs. 12% of added litter-C). We extend the notion of the priming effect from primarily a negative role promoting losses of native SOC, to a functional role that can replenish persistent SOC. Synthesis. Our measurements raise the possibility that, in species-rich forests, high- and low-quality litter decomposition play opposite but dynamically complementary roles in renewing POM—both by inducing its decomposition and formation—while exclusively favoring MAOM formation, which can help explain how differences in litter quality favor SOC accumulation and persistence. Global change factors that shift plant community composition may ultimately affect the fate of soil C, as changes in litter quality may force soil transitions from sinks to sources or sources to sinks of atmospheric CO2.

opencc-zeroJul 2023View details →

Data from: Soil microbes mediate the effects of resource variability on plant invasion

A fundamental question in ecology is which species will prevail over others amid changes in both environmental mean conditions and their variability. Although the widely accepted fluctuating resource hypothesis predicts that increases in mean resource availability and variability therein will promote non-native plant invasion, it remains unclear to what extent these effects might be mediated by soil microbes. We grew eight invasive non-native plant species as target plants in pot-mesocosms planted with five different synthetic native communities as competitors and assigned them to eight combinations of two nutrient-fluctuation (constant vs pulsed), two nutrient-availability (low vs high) and two soil-microbe (living vs sterilized) treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of non-native plants under overall low nutrient availability, whereas the nutrient fluctuation had minimal effect under high nutrient availability. In contrast, when plants grew in living soil, nutrient fluctuation promoted the dominance of non-native plants under high nutrient availability rather than under low nutrient availability. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the relative abundance of the most dominant pathogenic fungal family or genus under high nutrient availability, while decreasing it under low nutrient availability. Our findings are the first to indicate that besides its direct effect, environmental variability could also indirectly affect plant invasion via changes in soil microbial communities.

opencc-zeroJul 2023View details →

Data from: Soil nutrient heterogeneity alters productivity and diversity of experimental plant communities under multiple global change factors

Plant communities in nature are often challenged by multiple global change factors (GCFs) and also ubiquitously encountered with soil nutrient heterogeneity. So far, however, we know little about the interactive effect of multiple GCFs and soil nutrient heterogeneity on plant communities. We conducted an outdoor mesocosm experiment in which a plant community was either grown in heterogeneous soils consisting of high- and low-nutrient patches, or in homogeneous soils where the same amount of nutrients was evenly distributed. These plant communities were exposed to none (control), single, or a combination of two or four GCFs (i.e., drought, nitrogen deposition, microplastic and cadmium). Biomass of the plant community exposed to drought and nitrogen deposition were greater in heterogeneous than in homogeneous soils, but evenness of the plant community exposed to microplastics was lower. Increasing the number of GCFs increased community biomass more in heterogeneous than in homogeneous soils, but it generally reduced community evenness, independent of soil nutrient heterogeneity. These contrasting responses were related to changing competitive hierarchies and root foraging responses under different treatments. Our results suggest that soil nutrient heterogeneity can alter community productivity and diversity via changing competitive interactions of the component species, depending on both the identity and the number of GCFs acting on the community. These results have important implications for the maintenance of ecosystem functions and services under rapid and complex ongoing global changes.

opencc-by-4.0Jul 2023View details →

BSFFP, BSFFA, CPC, Control Treatment/No Fertilizer - Fertilizers, Post-harvest Soils, Amaranthus dubius Post-harvest Nutritional Values, Potting Soil Medium Chemical Analyses Raw Data

BSFFP (Plant-based wastes Feeding Substrate BSFF frass), BSFFA (Animal-based wastes Feeding Substrate BSFF frass), CPC (Commercial Plant-based Compost Fertilizer), Control Treatment/No Fertilizer Amaranthus dubius Nutritional Values, Potting Soil Medium Chemical Analyses Raw Data - Nitrification and Nitrate Uptake Properties. - Agronomy MDPI 2023.

opencc-by-4.0Aug 2023View details →

Soil CO2 Flux Data from the southern Malawi Rift

Soil CO2 data collected in transects across faults in the southern Malawi Rift in August 2018. Measurements of soil CO2 flux were collected during a survey in August 2018 during the dry season in Malawi, in order to attempt to reduce the possibility of a high biogenic flux obscuring the output of deeper CO2. We collected measurements using the accumulation chamber method (Chiodini et al., 1998), where a soil collar is coupled to the ground surface, and the gas flux is sampled and analysed for CO2 using a PP Systems EGM-4 Environmental Gas Analyser and a SRC-1 Soil Respiration Chamber. A high-resolution digital elevation model (DEM; 12.5 m TanDEM-X), was used to identify active fault scarps in southern Malawi (following Wedmore et al., 2020), which were the focus of our investigation. We collected flux measurements running from the footwall across the active faults and into the hanging wall of the scarps that we identified, with approximately 10-50 m spacing between individual sampling locations. Also published here is an ipython notebook to analyse the data.

opencc-by-4.0Aug 2023View details →

Data for Torppa et al. 2023 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety'

The dataset consists of the data that supports the findings of the article 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety’ written by Torppa et al. and published in Plant and Soil in 2023. The data consists of arbuscular mycorrhizal colonization, fatty acid and community data, as well as soil and crop nutrient and yield data.

Soil and census data of Heishiding plot

Intransitive competition has long been acknowledged as a potential mechanism favoring species coexistence. However, its prevalence, variance along environmental gradients, and possible underlying mechanisms (trade-offs) in plant communities (especially in forests) has seldomly been examined. A recently developed "reverse-engineering" approach based on Markov Chain allows us to estimate competitive transition matrices and competitive intransitivity from observational abundance data. Using this approach, we estimated competitive intransitivity of five dominant species in a subtropical forest and then related it to soil fertility (soil organic matter and soil pH) and demographic trade-offs (growth-survival and stature-recruitment trade-offs). In our forest plot, intransitive competition was common among the dominant species and peaked at the intermediate level of soil organic matter. Neither the growth-survival trade-off nor the stature-recruitment trade-off was positively related to competitive intransitivity. Our study for the first time empirically supported the unimodal intransitivity-fertility relationship in forests, which, however, was not mediated by the two demographic trade-offs in our plot.

opencc-zeroDec 2021View details →

Data for: Cessation of grazing causes biodiversity loss and homogenization of soil food webs

There is widespread concern that cessation of grazing in historically grazed ecosystems is causing biotic homogenization and biodiversity loss. We used 12 montane grassland sites along an 800-km north-south gradient across the United Kingdom, to test whether cessation of grazing affects local ɑ- and β-diversity of belowground food webs. We show cessation of grazing leads to strongly decreased ɑ-diversity of most groups of soil microbes and fauna, particularly of relatively rare taxa. In contrast, the β-diversity varied between groups of soil organisms. While most soil microbial communities exhibited increased homogenization after cessation of grazing, we observed decreased homogenization for soil fauna after cessation of grazing. Overall, our results indicate that exclusion of domesticated herbivores from historically grazed montane grasslands has far-ranging negative consequences for diversity of belowground food webs. This underscores the importance of grazers for maintaining the diversity of belowground communities, which play a central role in ecosystem functioning.

opencc-by-4.0Sep 2023View details →

TUdi-Vinedivers_Vineyard_Soil_Data_Austria

Dataset of soil properties from the TUdi/Vinedivers vineyard management experiments in Austria

opencc-by-4.0Aug 2023View details →

Data supplementing Lichtenberg et al. (2023) Differential effects of soil conservation practices on arthropods and crop yields. Journal of Applied Entomology

This dataset contains data and scripts that supplement the publication Lichtenberg et al. Differential effects of soil conservation practices on arthropods and crop yields. J. Appl. Entomol. 147: 931-940. <a href="https://doi.org/10.1111/jen.13188">https://doi.org/10.1111/jen.13188</a> Please cite the above article if you use any of the included data or code. Files are described in README.md.

Data from: Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks

Plants can suppress the growth of other plants by modifying soil properties. These negative plant-soil feedbacks are often species-specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown. Here, we investigated if and how benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, influence plant-soil feedbacks. We find that three out of five tested crop species suppress maize (Zea mays) performance via negative plant-soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids is sufficient to restore the protective effect for benzoxazinoid-deficient mutants. Sterilization and re-inoculation experiments suggest that benzoxazinoid-mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates that its magnitude is context-dependent. In summary, our study demonstrates that plant secondary metabolites can confer resistance to negative plant-soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations in the future.

Data from: Photodegradation modifies microplastic effects on soil properties and plant performance

Microplastics in soil affect plant-soil systems depending on their shape and polymer type. However, previous research has not yet considered the effects of degraded plastics, which are the plastic materials actually present in the environment. We selected 8 microplastics representing different shapes (fibers, films and foams) and polymer types, and exposed them to UV-C degradation. Each microplastic was mixed with soil at a concentration of 0.4% (w/w). The phytometer Daucus carota grew in each pot. At harvest, soil properties and plant biomass were measured. Photodegradation altered microplastics physical and chemical properties, impacting plant-soil systems. Microplastics degradation effects on plant and soil were observed with fibers and foams, but there were negligible effects with films. The latter could be explained by the polymer structure of films and manufacturer's additives, potentially delaying their degradation. Degraded fibers increased soil respiration more than their non-degraded counterparts, as photodegradation increased the positive effects of fibers on soil water retention. The emergence of oxygenated groups during degradation may have increased the hydrophilicity of fibers, enhancing their ability to retain water. Degraded foams increased soil respiration, which could be related to the possible leaching of organic substances with lower partition coefficients, which may promote soil microbial activity. By contrast, degraded foams decreased soil aggregation, likely as degradation produced larger holes increasing their permeability. Also, the increase of hydrophilic molecules could have decreased soil particle cohesiveness. Degraded fibers and foams increased shoot and root mass as a result of microplastic effects on soil properties. Photodegraded microplastics affected root traits, which could be linked to microplastic effects on soil water status and plant coping strategies.

Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)

Serpentine soils exhibit extreme properties (e.g. high magnesium content) influencing plant growth and survival and have been repeatedly documented to promote adaptive edaphic differentiation in plants. Individuals from four pairs of nearby diploid and autotetraploid populations of Biscutella laevigata sampled on serpentine vs non-serpentine soils in a factorial design are used to assess the genetic and phenotypic changes associated with edaphic origin and ploidy level. Individual samples from natural populations were subjected to soil elemental analysis and genotyping using restriction site-associated DNA sequences (RAD-seq) to link genetic variation with contrasting soils and ploidy levels. In diploids, genetic variation was consistent with demographic contraction and a pattern of isolation by environment with respect to the ratio of calcium / magnesium concentrations, whereas tetraploids presented evidence of expansion with limited edaphic differentiation. The genetic basis of tolerance and adaptation to serpentine was further assessed experimentally on seed-grown individuals from all populations subjected to high (serpentine-like) vs low (control) concentrations of magnesium in hydropony. Fitness-related phenotypic traits under experimental cultivation were consistent with adaptive differentiation among diploid ecotypes but not among the tetraploids that similarly grow in both habitats and consistently present higher investment in roots. Further work comparing experimentally resynthesized polyploids to natural diploids and polyploids has to tease the role of whole genome duplication apart from the impact of post-polyploidy evolution.

opencc-by-4.0Oct 2023View details →

A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil Dataset

This dataset contains the reference solutions used for training the two neural networks in 1-, 2- and 3-D cases for the article:"A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil" by Zeyuan Song and Zheyu Jiang, submitted to the journal Water Resources Research.  This dataset which describes the relationship between the pressure head and number of particles used to train two MLPs in D-GRW based solvers consists of three files, i.e., 1-, 2- and 3-D case study. There are two parts, original reference solutions and reference solutions, corresponding to the original solutions generated by coarse mesh solvers and solutions after data augmentation process, respectively.The dataset is generated by GRW based solvers and simulation results (e.g., Celia's finite difference method). Original reference solutions admit GRW proportionality assumption. We initialize the number of particles by multiplying the initial condition and 1E10.

opencc-by-4.0May 2023View details →

Greenhouse gas emissions from drained organic forest soils data

Compiled published peer-reviewed CO2, CH4 and N2O data on drained organic forest soils in boreal and temperate zones.

opencc-zeroOct 2023View details →

Data from: Revealing biogeographic patterns in genetic diversity of native and invasive plants and their association with soil community diversity in the Chinese coast

Within-species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through 'pre-adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic-species diversity relationship. Here, we selected a widespread native species (Phragmites australis) and its co-occurring invasive competitor (Spartina alterniflora) as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora, the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic-species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.

opencc-zeroOct 2023View details →

Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics

Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross-kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial-fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterized soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighboring evergreen broadleaf forest. Carbon (C) mineralization combined with five C-degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial-fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial-fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+−N), nitrate nitrogen (NO3−−N), and available phosphorus (AP). Structural equation modeling indicated that the potential cross-kingdom competition, based on the ratio of negative bacterial-fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C-degrading enzymatic activities and C mineralization. Synthesis and applications: Our results highlight the regulatory role of the negative bacterial-fungal association in enhancing the correlation between bacterial diversity and C mineralization. This suggests that promoting short-term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial-fungal negative associations to mediate carbon mineralization in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.

opencc-by-4.0Oct 2023View details →

Data from: Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients

Data associated with 'Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients' by Butler, Manzoni, and Warren, published in The ISME Journal (accepted 28/9/2023).

opencc-zeroDec 2023View details →

Data from: Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application

Fumigants and fungicides are effective at controlling soil-borne pathogens but might also adversely affect soil beneficial microbes, such as soil phosphorus (P) solubilizing microbes, further altering nutrient cycling processes. Therefore, this study investigated the effects of the fumigant chloropicrin (CP) and the fungicide azoxystrobin (AZO) on soil microeukaryotes and P-cycling related soil bacteria through a greenhouse experiment. Soil microeukaryotic communities and bacterial communities containing two phosphomonoesterase encoding genes (phoC and phoD) were analysed using high-throughput sequencing methods. Results showed that, when applied at the field recommended application dosage, the fungicide AZO had no significant influence on the community structure of soil microeukaryotes and phoD-containing bacteria. However, in CP-fumigated soils, the soil microeukaryotic community composition changed from fungi-dominated to protist-dominated. CP fumigation significantly decreased the total phoC/phoD gene copy number but increased the relative abundance of some phoC/phoD-containing bacteria (such as Sinorhizobium and Streptomyces), which are significantly positively correlated to available P compositions in soil. The structural equation model (SEM) confirmed that CP fumigation could affect soil available P content directly by altering phoC-/phoD-containing bacteria, or indirectly by affecting phoC/phoD gene abundance and acid/alkaline phosphatases activity in soil. The inconsistent changes in phoC/phoD-containing bacteria, phoC/phoD gene number, and the phosphomonoesterase activities indicated that enzyme secretion may not be the only way for P solubilizing soil microorganisms to regulate P availability after soil fumigation. The outcome of this study can provide theoretical support for the design of soil beneficial microorganism recovery strategies and the regulation of phosphate fertilizer after soil fumigation.