Dataset Information

16S characterization of microbiomes from Salton Sea Trough mud volcanoes and seeps

ABSTRACT: 16S characterization of microbiomes from Salton Sea Trough mud volcanoes and seeps Metagenome

PROVIDER: PRJNA891239 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22034811_1.fastq.gz	Fastqsanger.gz
	SRR22034811_2.fastq.gz	Fastqsanger.gz
	SRR22034812_1.fastq.gz	Fastqsanger.gz
	SRR22034812_2.fastq.gz	Fastqsanger.gz
	SRR22034813_1.fastq.gz	Fastqsanger.gz

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Project description:Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.

Project description:Purpose:The mud crab Scylla paramamosain is an economically important marine crab in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Vibrio Parahaemolyticus, resulting in great economic losses. However, the mechanisms involved in the immune response of this crab to bacterial infection are not fully understood. To understand the molecular mechanisms underlying the immune response to such pathogenic bacteria, we used high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the mud crab S.paramamosain infected with V.parahaemolyticus. Methods: The hemocytes sampled at 0-24h after infection with V.parahaemolyticus were used for transcriptome analysis. The hemocytes sampled at 24 h after injections with V.parahaemolyticus and no injected 0h(as control) were used for gene expression profiling analysis. Results: A total of 52,934,042 reads were obtained and assembled into 186,193 contigs in transcriptional responses of the V.parahaemolyticus-infected mud crab. Via annotation to the NCBI database and the Swissprot database, we obtained 48,934 identified unigenes. In total, 10,139(20.7%) unigenes were classified into Gene Ontology, and 25,349 unigenes were found in 20 KEGG categories. These genes included representatives from almost all functional categories. By using Solexa/Illumina's DeepSAGE, 1213 differentially expressed genes (P value < 0.05) were detected in comparative analysis of the expression profiles between V.parahaemolyticus-infected crabs and control crabs, including 538 remarkably upregulated genes and 675 remarkably downregulated genes. Conclusions: Based on our results, we conclude that the inflammatory response may play an important role in the early stages of infection. The signaling cascades such as the chemokine, JAK-STAT, and MAPK pathways are regulated by V.parahaemolyticus infection. These results revealed changes of multiple signaling pathways involved in immunity during V.parahaemolyticus infection, which will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection in the mud crab.

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16S characterization of microbiomes from Salton Sea Trough mud volcanoes and seeps

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