Ontology highlight
ABSTRACT:
PROVIDER: PRJNA871755 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21147480_1.fastq.gz | Fastqsanger.gz | |||
| SRR21147480_2.fastq.gz | Fastqsanger.gz | |||
| SRR21147481_1.fastq.gz | Fastqsanger.gz | |||
| SRR21147481_2.fastq.gz | Fastqsanger.gz | |||
| SRR21147482_1.fastq.gz | Fastqsanger.gz |
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Project description:Although hydrogen sulfide is toxic to most organisms, a fish, Poecilia mexicana, has adapted to survive in environments with high levels of hydrogen sulfide. The epigenetic changes in response to this environmental stress were examined by assessing DNA methylation alterations in the nucleated red blood cells (RBC) in the fish. In addition to collecting wild males and females from sulfidic and non-sulfidic environments, wild males and females in these environments were collected and moved to a non-sulfidic environment in the laboratory and propagated for two generations in a non-sulfidic environment. We compared epimutations between sexes and field and laboratory populations. The F0 generation sulfidic wild fish were compared to the non-sulfidic wild fish and found to have significant differential DNA methylation regions (DMRs) in the RBC DNA. The F2 generation laboratory fish were also compared between the sulfidic and non-sulfidic populations, and a significant number of DMRs were also identified. The DMRs have stable generational inheritance in the absence of the sulfidic environment. The DMRs in the F0 generation wild fish had an over 80% overlap with the F2 generation laboratory non-sulfidic environment propagated fish. This is one of the first examples of epigenetic generational stability after the removal of an environmental stressor. The DMR associated genes were found to be relevant to sulfur toxicity and metabolism processes.
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Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
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Project description:an autotrophic, elemental sulfur disproportionating bacterium
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Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.
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Project description:We reported the microbial communities in the biofilm anoxic-oxic-MBR system operated with different carbon source types.
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Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3)
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Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals.
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Project description:Eukaryotes may experience oxygen deprivation under several physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all the eukaryotes studied so far evolved ways to conserve energy via suppression of metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is poorly studied. One such animal is the symbiotic marine nematode Laxus oneistus. This thrives, invariably coated by its sulfur-oxidizing bacterium Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, by applying transcriptomics and proteomics, we discovered that, irrespective of the oxygen concentration it is subjected to, this nematode is mostly and constitutively engaging in ubiquitination-mediated proteolysis, energy generation, oxidative stress response and immune response. Furthermore, by incubating L. oneistus under sulfidic anoxic or hypoxic conditions, we found that, under the first condition, the worm upregulated genes involved in ribosome biogenesis, proteolytic systems (autophagy and the ubiquitin-proteasome system), chaperones, detoxification and lectins. Degradation pathways were likely induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients, whereas lectins were likely expressed to promote the attachment of its anaerobic, thiotrophic symbiont. Besides, L. oneistus appeared to survive oxygen deprivation by using alternative electron carriers (rhodoquinone) and acceptors (fumarate) to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., development, amino acid biosynthesis, feeding behaviour, mating) were upregulated. Intriguingly, the worm’s Toll-like innate immunity pathway and a number of immune effectors (e.g., Bacterial Permeability Increasing proteins, fungicides) were upregulated in the presence of oxygen. In conclusion, we hypothesize that L. oneistus survives in anoxic sulfidic sand by overexpressing degradation processes, rewiring oxidative phosphorylation and by reinforcing its coat of bacterial sulfur-oxidizers. In the presence of oxygen, instead, it appears to exploit glycolysis to eat, mate and grow. Moreover, oxygen appears to affect L. oneistus immune system in such way, as to favor specific attachment of its anaerobic partner in anoxia and to produce broad-range antimicrobials when oxygen is present.
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