Microbial communities inhabiting acidic mine-degraded soils
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PROVIDER: PRJEB28850 | ENA |
REPOSITORIES: ENA
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Project description:Mining of mineral resources substantially alters both the above and below-ground soil ecosystem, which then requires rehabilitation back to a pre-mining state. For belowground rehabilitation, recovery of the soil microbiome to a state which can support key biogeochemical cycles, and effective plant colonization is usually required. One solution proposed has been to translate microbial inocula from agricultural systems to mine rehabilitation scenarios, as a means of reconditioning the soil microbiome for planting. Here, we experimentally determine both the aboveground plant fitness outcomes and belowground soil microbiome effects of a commercially available soil microbial inocula (SMI). We analyzed treatment effects at four levels of complexity; no SMI addition control, Nitrogen addition alone, SMI addition and SMI plus Nitrogen addition over a 12-week period. Our culture independent analyses indicated that SMIs had a differential response over the 12-week incubation period, where only a small number of the consortium members persisted in the semi-arid ecosystem, and generated variable plant fitness responses, likely due to plant-microbiome physiological mismatching and low survival rates of many of the SMI constituents. We suggest that new developments in custom-made SMIs to increase rehabilitation success in mine site restoration are required, primarily based upon the need for SMIs to be ecologically adapted to both the prevailing edaphic conditions and a wide range of plant species likely to be encountered.
| S-EPMC6636552 | biostudies-literature
Project description:Miscanthus × giganteus is a giant C4 grass native to Asia. Unlike most C4 species, it is relatively cold tolerant due to adaptations across a wide range of altitudes. These grasses are characterized by high productivity and low input requirements, making them excellent candidates for bioenergy feedstock production. The aim of this study was to investigate the potential for growing Miscanthus on extremely marginal soils, degraded by open lignite (brown coal) mining. Field experiments were established within three blocks situated on waste heaps originating from the lignite mine. Analyses were conducted over the first 3 years following Miscanthus cultivation, focusing on the effect of organic and mineral fertilization on crop growth, development and yield in this extreme environment. The following levels of fertilization were implemented between the blocks: the control plot with no fertilization (D0), a plot with sewage sludge (D1), a plot with an identical amount of sewage sludge plus one dose of mineral fertilizer (D2) and a plot with an identical amount of sewage sludge plus a double dose of mineral fertilizer (D3). Crop development and characteristics (plant height, tillering, and biomass yield [dry matter]) were measured throughout the study period and analyzed using Analysis of Variance (ANOVA). Significant differences were apparent between plant development and 3rd year biomass production over the course of the study (0.964 kg plant-1 for DO compared to 1.503 kg plant-1 for D1). Soil analyses conducted over the course of the experiment showed that organic carbon levels within the soil increased significantly following the cultivation of Miscanthus, and overall, pH decreased. With the exception of iron, macronutrient concentrations remained stable throughout. The promising yields and positive effects of Miscanthus on the degraded soil suggests that long term plantations on land otherwise unsuitable for agriculture may prove to be of great environmental and economic significance.
| S-EPMC5466985 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE38456: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (lab study) GSE38458: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (field study) Refer to individual Series
2012-08-31 | E-GEOD-38474 | biostudies-arrayexpress
Project description:Our research goal is to illustrate the potential of gene expression profiling to discriminate between polluted and non-polluted field sites and predict the presence of a specific contaminant. Using a gene expression analysis, we challenged our custom Daphnia magna cDNA microarray to determine the presence of a specific metal toxicant in blinded field samples collected from two copper mines in California. We compared the gene expression profiles from our field samples to previously established expression profiles for Cu, Cd, and Zn. The expression profiles from the Cu containing field samples clustered with the Cu specific gene expression profiles. Many of the previously discovered copper biomarkers were also differentially expressed in the field samples, suggesting that gene expression analysis is capable of producing robust biomarkers of exposure, which can be validated in field studies. In addition, our study revealed that upstream field samples containing undetectable levels of Cu caused the differential expression of only a few genes, lending support for the concept of a No Observed Transcriptional Effect Level (NOTEL). If confirmed by further studies, the NOTEL may play an important role in discriminating polluted and non-polluted sites in future monitoring efforts. Keywords: ecotoxicogenomic exposure study
2008-06-09 | GSE7667 | GEO
Project description:Our research goal is to illustrate the potential of gene expression profiling to discriminate between polluted and non-polluted field sites and predict the presence of a specific contaminant. Using a gene expression analysis, we challenged our custom Daphnia magna cDNA microarray to determine the presence of a specific metal toxicant in blinded field samples collected from two copper mines in California. We compared the gene expression profiles from our field samples to previously established expression profiles for Cu, Cd, and Zn. The expression profiles from the Cu containing field samples clustered with the Cu specific gene expression profiles. Many of the previously discovered copper biomarkers were also differentially expressed in the field samples, suggesting that gene expression analysis is capable of producing robust biomarkers of exposure, which can be validated in field studies. In addition, our study revealed that upstream field samples containing undetectable levels of Cu caused the differential expression of only a few genes, lending support for the concept of a No Observed Transcriptional Effect Level (NOTEL). If confirmed by further studies, the NOTEL may play an important role in discriminating polluted and non-polluted sites in future monitoring efforts. Keywords: ecotoxicogenomic exposure study
2008-06-09 | GSE7666 | GEO
Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
2016-12-10 | GSE91083 | GEO
Project description:A mixotrophic and acidophilic bacterial strain BGR 140T was isolated from mine tailings in the Harz Mountains near Goslar, Germany. Cells of BGR 140T were Gram-stain-positive, endospore-forming, motile and rod-shaped. BGR 140T grew aerobically at 25-55 °C (optimum 45 °C) and at pH 1.5-5.0 (optimum pH 3.0). The results of analysis of the 16S rRNA gene sequences indicated that BGR 140T was phylogenetically related to different members of the genus Sulfobacillus, and the sequence identities to Sulfobacillus acidophilus DSM 10332T, Sulfobacillus thermotolerans DSM 17362T, and Sulfobacillus benefaciens DSM 19468T were 94.8, 91.8 and 91.6 %, respectively. Its cell wall peptidoglycan is A1γ, composed of meso-diaminopimelic acid. The respiratory quinone is DMK-6. The major polar lipids were determined to be glycolipid, phospholipid and phosphatidylglycerol. The predominant fatty acid is 11-cycloheptanoyl-undecanoate. The genomic DNA G+C content is 58.2 mol%. On the basis of the results of phenotypic and genomic analyses, it is concluded that strain BGR 140T represents a novel species of the genus Sulfobacillus, for which the name Sulfobacillus harzensis sp. nov. is proposed because of its origin. Its type strain is BGR 140T (=DSM 109850T=JCM 39070T).
| S-EPMC8489842 | biostudies-literature
Project description:Natural remediation of dye-polluted river sediment
| PRJDB4716 | ENA
Project description:Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 106 to 1.81 × 109 and 4.81 × 106 to 4.54 × 108 copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a 15N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g-1 h-1, contributing 16.67-53.27% to N2 production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China.
| S-EPMC6134040 | biostudies-literature
Project description:Acid mine drainage (AMD) microbial communities contain microbial eukaryotes (both fungi and protists) that confer a biofilm structure and impact the abundance of bacteria and archaea and the community composition via grazing and other mechanisms. Since prokaryotes impact iron oxidation rates and thus regulate AMD generation rates, it is important to analyze the fungal and protistan populations. We utilized 18S rRNA and beta-tubulin gene phylogenies and fluorescent rRNA-specific probes to characterize the eukaryotic diversity and distribution in extremely acidic (pHs 0.8 to 1.38), warm (30 to 50 degrees C), metal-rich (up to 269 mM Fe(2+), 16.8 mM Zn, 8.5 mM As, and 4.1 mM Cu) AMD solutions from the Richmond Mine at Iron Mountain, Calif. A Rhodophyta (red algae) lineage and organisms from the Vahlkampfiidae family were identified. The fungal 18S rRNA and tubulin gene sequences formed two distinct phylogenetic groups associated with the classes Dothideomycetes and Eurotiomycetes. Three fungal isolates that were closely related to the Dothideomycetes clones were obtained. We suggest the name "Acidomyces richmondensis" for these isolates. Since these ascomycete fungi were morphologically indistinguishable, rRNA-specific oligonucleotide probes were designed to target the Dothideomycetes and Eurotiomycetes via fluorescent in situ hybridization (FISH). FISH analyses indicated that Eurotiomycetes are generally more abundant than Dothideomycetes in all of the seven locations studied within the Richmond Mine system. This is the first study to combine the culture-independent detection of fungi with in situ detection and a demonstration of activity in an acidic environment. The results expand our understanding of the subsurface AMD microbial community structure.
| S-EPMC522060 | biostudies-literature