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32 results for “Soil microorganisms”
Dataset for "Fertilizer value of dairy processing waste materials and contributions of soil microorganisms towards phosphorus uptake in grasses."
<p>This file includes the dataset used for the analysis of the fertilizer value from dairy processing waste materials and the contribution of soil microorganisms towards P uptake. More information in the linked future publication</p>
Data from: Eco–enzymatic stoichiometry unveils resource limitations in soil microorganisms during subtropical vegetation restoration
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Soil depth matters: Shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils
<p>Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.</p>
Effects of past and present-day landscape structure on forest soil microorganisms
<p><span><span><span><span><span><span><span><span><span><span><span>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.</span></span></span></span></span></span></span></span></span></span></span></p>
Raw sequence data and OTU tables of soil microorganisms obtained across a summit in the Lesotho highlands
<p>Mountain regions represent unique environments characterized by strong topographical diversity which drive climatic and environmental variability within these environments. These regions thus provide an opportunity to explore the relationships between various environmental factors and soil microorganisms. In this study, we investigated the impact of micro-topographical (i.e., north/south-facing slope aspects and flat plateau between them) variations on microbial diversity and community structures across a Lesotho mountain summit.</p> <p>Raw sequenced data were generated using the Illumina MiSeq platform on DNA extracted from soil samples collected across the plateau, north- and south-facing slopes. This data was then used for taxonomic classification of the bacterial and fungal OTUs for the determination of the alpha- and beta-diversity across the slopes. These analyses revealed that a relatively greater bacterial and fungal diversity could be observed for the north-facing slope compared to the south-facing slope and plateau. While there was no difference in group variance of bacterial and fungal community structures across the plateau, north- and south-facing slopes.</p> <p>Multiple comparison analyses were conducted to determine the impact of various abiotic and geographical factors on bacterial and fungal diversity and community structures. These analyses indicated that the slope aspect significantly affects bacterial and fungal community structures at this location. These results provide an original insight into soil microbial diversity in the Lesotho highlands and offer an opportunity to investigate the response of soil microorganisms to changes in environmental and climatic factors in highly variable mountain environments such as the Lesotho highlands.</p>
Sample microscopic images of soil microorganism
<p>The images within this repository contains raw, unprocessed, microscopic images of soil fungi belonging to the following genera: Fusarium, Trichoderma, Verticillium, and Chromista of the Phytophthora genus that filenames contain name of the genus followed by underscore and number of an image for a given genera. Each image is labeled based on the specific microorganism genus it represents. The subimages images contains retrieved subimages, where each subimage corresponds to a single object that contains fragments of a microorganism. The subimages are generated from the original images and follow a specific naming convention. The image name indicates the microorganism genus, followed by information about the input image it was generated from, and finally the number of the retrieved subimage from that input image.</p> <p>These subimages are utilized for training purposes using the Transfer Learning method with the CNN model called ResNet50.</p> <p>This repository is provided as a Supplementary Material to the article "Automated Identification of Soil Fungi and Chromista through Convolutional Neural Networks" submitted to the <a href="https://www.sciencedirect.com/journal/engineering-applications-of-artificial-intelligence">Engineering Applications of Artificial Intelligence</a> journal.</p>
Supplementary material/Organic carbon dynamics in clay soils: impact of management practices on microorganism structure and abundance under semi-arid conditions
<p>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<sup>-1</sup>. This was followed by the amended plot and the conventional plot, respectively, with 43 Mg ha<sup>-1</sup> and 38 Mg ha<sup>-1</sup>. 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.</p>
Data from: Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application
<p>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 (<em>phoC</em> and <em>phoD</em>) 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 <em>phoD</em>-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 <em>phoC</em>/<em>phoD</em> gene copy number but increased the relative abundance of some <em>phoC</em>/<em>phoD</em>-containing bacteria (such as <em>Sinorhizobium</em> and <em>Streptomyces</em>), 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 <em>phoC</em>-/<em>phoD</em>-containing bacteria, or indirectly by affecting <em>phoC</em>/<em>phoD</em> gene abundance and acid/alkaline phosphatases activity in soil. The inconsistent changes in <em>phoC</em>/<em>phoD</em>-containing bacteria, <em>phoC</em>/<em>phoD</em> 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.</p>
Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms
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Effects of past and present-day landscape structure on forest soil microorganisms
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Global patterns of nutrient limitation in soil microorganisms
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Data from: Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application
Open the record for dataset details and reuse information.
Raw sequence data and OTU tables of soil microorganisms obtained across a summit in the Lesotho highlands
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Soil pH: The Effect of Nitrogen Addition and Different pH Levels on Microorganism Populations
The purpose of this experiment was to measure the effect of NH4NO3 addition and different levels of pH on microorganism populations. The experiment was located in field B. This experiment was laid out as a full factorial design with 3 nitrogen levels and 4 pH levels. The pH levels strived for are 4.0, 5.5, 6.5, and controls. The nitrogen levels are E, G, and I are defined in fertilization details. The experiment had 4 replicates. The treatments were randomly assigned to the 48 plots. The plots were 4 by 4 meters and were laid out in a 6 by 8 grid. On May 5, 1995, a wildfire burned all of the plots in experiment 24 in field B.
Soil ammonium: The Effect of Nitrogen Addition and Different pH Levels on Microorganism Populations
The purpose of this experiment was to measure the effect of NH4NO3 addition and different levels of pH on microorganism populations. The experiment was located in field B. This experiment was laid out as a full factorial design with 3 nitrogen levels and 4 pH levels. The pH levels strived for are 4.0, 5.5, 6.5, and controls. The nitrogen levels are E, G, and I are defined in fertilization details. The experiment had 4 replicates. The treatments were randomly assigned to the 48 plots. The plots were 4 by 4 meters and were laid out in a 6 by 8 grid. On May 5, 1995, a wildfire burned all of the plots in experiment 24 in field B.
Soil nitrate: The Effect of Nitrogen Addition and Different pH Levels on Microorganism Populations
The purpose of this experiment was to measure the effect of NH4NO3 addition and different levels of pH on microorganism populations. The experiment was located in field B. This experiment was laid out as a full factorial design with 3 nitrogen levels and 4 pH levels. The pH levels strived for are 4.0, 5.5, 6.5, and controls. The nitrogen levels are E, G, and I are defined in fertilization details. The experiment had 4 replicates. The treatments were randomly assigned to the 48 plots. The plots were 4 by 4 meters and were laid out in a 6 by 8 grid. On May 5, 1995, a wildfire burned all of the plots in experiment 24 in field B.
Data from: Belowground community responses to fire: meta-analysis reveals contrasting responses of soil microorganisms and mesofauna
Global fire regimes are shifting due to climate and land use changes. Understanding the responses of belowground communities to fire is key to predicting changes in the ecosystem processes they regulate. We conducted a comprehensive meta-analysis of 1634 observations from 131 empirical studies to investigate the effect of fire on soil microorganisms and mesofauna. Fire had a strong negative effect on soil biota biomass, abundance, richness, evenness, and diversity. Fire reduced microorganism biomass and abundance by up to 96%. Bacteria were more resistant to fire than fungi. Fire reduced nematode abundance by 88% but had no significant effect on soil arthropods. Fire reduced richness, evenness and diversity of soil microorganisms and mesofauna by up to 99%. We found little evidence of temporal trends towards recovery within 10 years post-disturbance suggesting little resilience of the soil community to fire. Interactions between biome, fire type, and depth explained few of these negative trends. Future research at the intersection of fire ecology and soil biology should aim to integrate soil community structure with the ecosystem processes they mediate under changing global fire regimes.
Data from: A native parasitic plant and soil microorganisms facilitate a native plant co-occurrence with an invasive plant
Invasive plants often interact with antagonists that include native parasitic plants and pathogenic soil microbes, which may reduce fitness of the invaders. However, to date, most of the studies on the ecological consequences of antagonistic interactions between invasive plants and the resident biota focused only on pairwise interactions. A full understanding of invasion dynamics requires studies that test the effects of multiple antagonists on fitness of invasive plants and co-occurring native plants. Here, we used an invasive plant Mikania micrantha, a co-occurring native plant Coix lacryma-jobi, and a native holoparasitic plant Cuscuta campestris to test whether parasitism on M. micrantha interacts with soil fungi and bacteria to reduce fitness of the invader and promote growth of the co-occurring native plant. In a factorial set up, M. micrantha and C. lacryma-jobi were grown together in pots in the presence versus absence of parasitism on M. micrantha by C. campestris, and in the presence versus absence of full complements of soil bacteria and fungi. Fungicide and bactericide were used to suppress soil fungi and bacteria, respectively. Findings show that heavy parasitism by C. campestris caused the greatest reduction in M. micrantha biomass when soil fungi and bacteria were suppressed. In contrast, the co-occurring native plant C. lacryma-jobi experienced the greatest increase in biomass when grown with heavily parasitized M. micrantha and in the presence of a full complement of soil fungi and bacteria. Taken together, our results suggest that selective parasitism on susceptible invasive plants by native parasitic plants and soil microorganisms may diminish competitive ability of invasive plants and facilitate native plant co-existence with invasive plants.
Root traits and soil microorganisms as drivers of plant-soil feedbacks within the sub-arctic tundra meadow
<p>Plant-soil feedback (PSF) can influence the composition of various soil microorganisms (antagonistic and mutualistic), which can have reciprocal effects on plants. At the same time, we do not understand the effects of fine root traits in moderating microbial-driven PSF. We therefore conducted a greenhouse study to aid in understanding the relationship between root traits, soil community composition (PLFAs and high-throughput sequencing data) and plant-soil feedback (PSF). These data therefore include datasets with fine root traits, raw sequence reads from high-throughput sequencing for soil fungi, phospholipid fatty acid data and biomass data after the plant-soil feedback study.</p>
Data from: Do microorganism stoichiometric alterations affect carbon sequestration in paddy soil subjected to phosphorus input?
Ecological stoichiometry provides a powerful tool for integrating microbial biomass stoichiometry with ecosystem processes, opening far-reaching possibilities for linking microbial dynamics to soil carbon (C) metabolism in response to agricultural nutrient management. Despite its importance to crop yield, the role of phosphorus (P) with respect to ecological stoichiometry and soil C sequestration in paddy fields remains poorly understood, which limits our ability to predict nutrient-related soil C cycling. Here, we collected soil samples from a paddy field experiment after 7 years of superphosphate application along a gradient of 0, 30, 60, 90 (P-0 through P-90, respectively) kg P ha-1 y-1 in order to evaluate the role of exogenous P on soil C sequestration through regulating microbial stoichiometry. P fertilization increased soil total organic C and labile organic C by 1-14% and 4-96%, respectively, while rice yield is a function of the activities of soil β-1, 4-glucosidase (BG), acid phosphatase (AP) and the level of available soil P through a stepwise linear regression model. P input induced C limitation as reflected by decreases in the ratios of C:P in soil and microbial biomass. An ecoenzymatic ratio indicating microbial investment in C versus P acquisition, i.e., ln(BG):ln(AP), changed the ecological function of microbial C acquisition and was stoichiometrically related to P input. This mechanism drove a shift in soil resource availability by increasing bacterial community richness and diversity, and stimulated soil C sequestration in the paddy field by enhancing C degradation-related bacteria for the breakdown of plant-derived carbon sources. Therefore, the decline in the C:P stoichiometric ratio of soil microorganism biomass under P input was beneficial for soil C sequestration, which offered a "win-win" relationship for the maximum balance point between C sequestration and P availability for rice production in the face of climate change.
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