Ontology highlight
ABSTRACT:
PROVIDER: PRJNA988918 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25080500_1.fastq.gz | Fastqsanger.gz | |||
| SRR25080500_2.fastq.gz | Fastqsanger.gz | |||
| SRR25080501_1.fastq.gz | Fastqsanger.gz | |||
| SRR25080501_2.fastq.gz | Fastqsanger.gz | |||
| SRR25080502_1.fastq.gz | Fastqsanger.gz |
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Project description:The interaction of animals with microbes relies on the specific recognition of microbial-derived molecules by receptors of the immune system. Sponges (phylum Porifera), as sister group of the Eumetazoa, provide insights into conserved mechanisms for animal-microbe crosstalk, but empirical data is limited. Here we aimed to characterize the immune response of sponges upon microbial stimuli by RNA-Seq. Two sponges species from the Mediterranean Sea, Aplysina aerophoba and Dysidea avara, were challenged with microbial-associated molecular patterns (lipopolysaccharide and peptidoglycan) or sterile artificial seawater (control) in aquarium experiments. Sponge tissue samples were collected 1h, 3h, and 5h after treatment. The response of the sponges to the treatments was assessed by differential gene expression analysis of RNA-Seq data. For each species, we compared the transcriptomic profiles of the samples in MAMP treatment to control within each time point.
2018-11-26 | E-MTAB-6757 | biostudies-arrayexpress
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
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Project description:Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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Project description:Sulfur metabolism in the deep-sea cold seep has been mentioned to have an important contribution to the biogeochemical cycle of sulfur in previous studies. And sulfate reducing bacteria have also been considered to be a dominant microbial population in the deep-sea cold seep and play a crucial role in this process. However, most of sulfate reducing bacteria from cold seep still cannot be purely cultured under laboratory conditions, therefore the actual sulfur metabolism pathways in sulfate reducing bacteria from the deep-sea cold seep have remained unclear. Here, we isolate and pure culture a typical sulfate reducing bacterium Desulfovibrio marinus CS1 from the sediment sample of the deep-sea cold seep in the South China Sea, which provides a probability to understand the sulfur metabolism in the cold seep.
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Project description:<p>Marine sponges can host abundant and diverse microbiomes, which can largely influence the metabolism and other phenotypic traits of the host. However, information on the potential relationships between sponge microbiomes and metabolic signatures, other than secondary metabolites explored for biotechnological purposes, needs further investigation. Applying an integrated approach, we investigated the microbiomes associated with 4 ubiquitous Mediterranean sponge species (i.e., Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula), correlated with their metabolomic patterns (in terms of lipidomics) and microbial predicted functions. Microscopy observations of sponge tissues revealed differences in microbial abundances, which, however, were only partially linked to their diversity assessed through metabarcoding. The microbiomes of the 4 sponges showed a species-specific composition and a different core size, which was independent from the microbial diversity of the surrounding seawater. Predicted functions of the associated microbiomes allowed identifying 2 functional host clusters: one more related to heterotrophic pathways and the other more linked to phototrophic activities. Differences in the microbiomes were also associated with different metabolic profiles, mostly due to specific compounds characterizing the host and its microbiome. Overall, this study provides new insights on the functionality of sponges and their prokaryotic symbioses’, and in particular, it discloses a descriptive sketch of the diverse compartments forming the sponge holobiont.</p>
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Project description:Marine microorganisms inhabiting the bathypelagic zone (1000 m - 4000 m) are pivotal to biogeochemical cycling. However, a comprehensive understanding of microbial community structure and their metabolic activities adaptations to the extreme deep-sea conditions remains elusive. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities spanning the surface and bathypelagic layers of the South China Sea (SCS) and performed a comparative analysis with metagenomic data. The metaproteome and metagenome showed low correlation in functional expression but a high correlation at the phylum level. High-abundance genes were more likely to be translated into proteins, with protein over-representation observed in energy conversion and matter transport processes. Short-chain amide porins facilitate substance exchange and maintain cellular homeostasis, enabling Methylococcales to adapt to deep-sea conditions and actively oxidize methane. Flexible energy utilization strategies, such as CO oxidation, enable Propionibacteriales to thrive in deep-sea environments. This study highlights the significance of microbial enzyme resources and offers valuable insights into the adaptations of deep-sea microorganisms, emphasizing their considerable application potential.
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Project description:In the seabed, chemical defences mediate inter- and intraspecific interactions and may determine organisms’ success, shaping the diversity and function of benthic communities. Sponges represent a prominent example of chemically-defended marine organisms with great ecological success. The ecological factors controlling the production of their defensive compounds and the evolutionary forces that select for these defences remain little understood. Each sponge species produces a specific and diverse chemical arsenal with fish-deterrent, antifouling and antimicrobial properties. However, some small animals (mesograzers), mainly sea slugs, have specialized in living and feeding on sponges. Feeding on chemically-defended organisms provides a strategy to avoid predators, albeit the poor nutritional value of sponges. In order to investigate the mechanisms that control sponge chemical defence, with particular focus on the response to specialist grazers, we investigated the interaction between the sponge Aplysina aerophoba and the sea slug Tylodina perversa. Here we performed controlled experiments and collected sponge samples at different time points (3h, 1d and 6d after treatment). To further elucidate if the sponge response is specific to grazing by T. perversa, we also included a treatment in which sponges were mechanically damaged with a scalpel. We compared gene expression between treatments based on RNA-Seq data.
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Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
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