Composition of bacterial community in well H13 at Hainich Critical Zone Exploratory
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PROVIDER: PRJEB78701 | ENA |
REPOSITORIES: ENA
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Project description:Bacterial community structure in soils, seepage water and groundwater of the Hainich Critical Zone Exploratory
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Project description:Bacterial diversity in carbonate rock aquifers of the Hainich Critical Zone Exploratory
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Project description:Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5-4.7 nmol L-1 d-1, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L-1 oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.
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Project description:Composition of bacterial communities in seepage of forest and pasture soils of the Hainich Critical Zone Exploratory (Germany)
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Project description:<p>Understanding biogeochemical conversions of dissolved organic matter (DOM) in aquifers is paramount for the effective management of groundwater supplies. On its passage through the critical zone, DOM is subject to biogeochemical conversions and therefore carries cross-habitat information useful for monitoring and predicting the stability of groundwater ecosystem services. Groundwater metabolomics assesses this information. However, challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics, and the necessity to maintain analytical conditions for long-term monitoring. We explored fractured sedimentary bedrock by 5-year untargeted metabolomics monitoring for oxic perched and anoxic phreatic sites along a hillslope recharge area, to evaluate DOM as groundwater tracer. Dimension reduction by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels and environmental tracers. The metabolome was highly variable lacking seasonal patterns, and did not segregate by geographic location of sampling wells thus ruling out surface vegetation or (agricultura) land use as driving factor. The metabolome time series provide detailed insights into subsurface responses to recharge dynamics. Metabolomics monitoring provides information on groundwater flows, and allows concluding about below ground ecology and water quality evolution, required to understand the impact of interannual wet-dry cycles.</p><p><br></p><p>This study is an extension of groundwater monitoring untargeted <strong>MS1 data </strong>previously published in <a href='https://www.ebi.ac.uk/metabolights/MTBLS3450' rel='noopener noreferrer' target='_blank'><strong>MTBLS3450</strong></a> and <a href='https://www.ebi.ac.uk/metabolights/editor/MTBLS8433' rel='noopener noreferrer' target='_blank' style='color: currentcolor;'><strong>MTBLS8433</strong></a></p>
2024-10-17 | MTBLS11375 | MetaboLights
Project description:bacterial community composition Raw sequence reads
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Project description:Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes.
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Project description:The pervasiveness of gene expression variation and its contribution to phenotypic variation and evolution is well known. This gene expression variation is context dependent, with differences in regulatory architecture often associated with intrinsic and environmental factors, and is modulated by regulatory elements that can act in cis (linked) or in trans (unlinked) relative to the genes they affect. So far, little is known about how this genetic variation affects the evolution of regulatory architecture among closely related tissues during population divergence. To address this question, we analyzed gene expression in the midgut, hindgut, and Malpighian tubule as well as microbiome composition in the two gut tissues in four Drosophila melanogaster strains and their F1 hybrids from two divergent populations: one from the derived, European range and one from the ancestral, African range. In both the transcriptome and microbiome data, we detected extensive tissue- and genetic background-specific effects, including effects of genetic background on overall tissue specificity. Tissue-specific effects were typically stronger than genetic background-specific effects, although the two gut tissues were not more similar to each other than to the Malpighian tubules. An examination of allele specific expression revealed that, while both cis and trans effects were more tissue-specific in genes expressed differentially between populations than genes with conserved expression, trans effects were more tissue-specific than cis effects. Despite there being highly variable regulatory architecture, this observation was robust across tissues and genetic backgrounds, suggesting that the expression of trans variation can be spatially fine-tuned as well as or better than cis variation during population divergence and yielding new insights into cis and trans regulatory evolution.
2024-07-31 | GSE263264 | GEO
Project description:Study of bacterial diversity and community composition in artificial pit mud used for fermentation of Chinese Strong Flavor Liquor
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