Plankton communities from ruunig water ecosystem in Songhua River basin
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ABSTRACT:
PROVIDER: PRJNA477605 | ENA |
REPOSITORIES: ENA
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Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:Koshi River Basin raw sequences Metagenome
| PRJNA515965 | ENA
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50164 | biostudies-arrayexpress
Project description:We used single-cell sequencing data and imaging to investigate Eukaryotic plankton from environmental marine samples collected from Coogee, NSW, Australia.
2024-08-18 | GSE274796 | GEO
Project description:we applied metaproteomic approach to capture proteins from three size-fractionated microbial communities at the DCM in the basin of the South China Sea. The deep recovery of proteomes from a marine DCM plankton assemblage provides the highest resolution of metabolic activities as well as microbial niche differentiation, revealing a spectrum of biological processes carrying out by microbes at DCM of the SCS.
2020-12-21 | PXD016812 | Pride
Project description:Water, food, energy, and the ecosystems they depend on interact with each other in highly complex and interlinked ways. These interdependencies can be traced particularly well in the context of a river basin, which is delineated by hydrological boundaries. The interactions are shaped by humans interacting with nature, and as such, a river basin can be characterized as a complex, coupled socioecological system. The Niger River Basin in West Africa is such a system, where water infrastructure development to meet growing water, food, and energy demands may threaten a productive and vulnerable basin ecosystem. These dynamic interactions remain poorly understood. Trade-off analyses between different sectors and at different spatial scales are needed to support solution-oriented policy analysis, particularly in transboundary basins. This study assesses the impact of climate and human/anthropogenic changes on the water, energy, food, and ecosystem sectors and characterizes the resulting trade-offs through a set of generic metrics related to the sustainability of water availability. Results suggest that dam development can mitigate negative impacts from climate change on hydropower generation and also on ecosystem health to some extent.
| S-EPMC6473704 | biostudies-other
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.
2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress
Project description:Water and land resource utilization is an important driving force of changes in ecosystem services; therefore, research on multi-parameter coupling systems that consider "ecosystem services, water resources, and land resources" together has key significance for river basins. This study aims to reveal the interaction and mutual influence of ecosystem services and water and land resources in the Daguhe River Basin, China, based on the coupling coordination degree model. The results showed that during the period from 2000 to 2010, the coupling coordination degree values for the years 2000, 2005, and 2010 were 0.6005, 0.7292, and 0.8037. The corresponding coupling coordination classifications were categorized as "primary coordinated development", "intermediate coordinated development," and "well-coordinated development", respectively. These results reflected the fact that the relationship between water and land resource utilization and the environment tends to evolve in the direction of coordinated development (an improvement in one part corresponds to an improvement in another part) with variation in water and land utilization types, and eventually pushes the whole resource, as well as ecological and environmental systems, from low to high levels of coupling coordination degrees as observed in case of the Daguhe River Basin, China. Our research provides an overview of the interaction between ecosystem services and water and land resources in the Daguhe Basin and even in the Shandong Province. With our results, we offer new perspectives on river basin management and for planning future eco-environmental policies (the policy is specifically designed for the ecological environment) by combining water and land resource utilization.
| S-EPMC8432845 | biostudies-literature
Project description:Evaluating the potential human health and ecological risks associated with exposures to complex chemical mixtures in the environment is one of the main challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrate chemical monitoring and biological effects data to evaluate risks associated with specific chemicals present in the environment. In the present study water samples from five locations near two wastewater treatment plants in the St. Croix River basin on the border of MN and WI, USA were analyzed for 127 contaminants including wastewater indicators, pharmaceuticals, and a number of natural and synthetic steroids. Prior knowledge about chemical-gene interactions was used to develop site-specific knowledge assembly models (KAMs) that were used to formulate hypothesis concerning possible biological effects of exposure to the chemicals detected at each location and suggest assays and endpoints for follow-up investigation. Additionally empirical hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location using a high density oligonucleotide microarray. Empirical gene expression data were analyzed to identify functional annotation terms enriched among the lists of differentially-expressed probes. However, the general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses, based on prior knowledge.
2016-05-11 | GSE81263 | GEO
Project description:The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.
2022-06-01 | GSE185175 | GEO