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Sponge metagenome

ABSTRACT: Marine sponge-associated obligate symbionts Thaumarchaeota

PROVIDER: PRJNA495396 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR8088660_1.fastq.gz	Fastqsanger.gz
	SRR8088660_2.fastq.gz	Fastqsanger.gz
	SRR8088661_1.fastq.gz	Fastqsanger.gz
	SRR8088661_2.fastq.gz	Fastqsanger.gz

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Project description:Marine sponges are essential for coral reefs to thrive and harbour a diverse microbiome that is thought to contribute to host health. Although the overall function of sponge symbionts has been increasingly described, in-depth characterisation of each taxa remains challenging, with many sponge species hosting up to 3,000 distinct microbial species. Recently, the sponge Ianthella basta has emerged as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other minor taxa. Here, we retrieved metagenome assembled genomes (MAGs) for >90% of I. basta’s microbial community which allowed us to make a complete metabolic reconstruction of the sponge’s microbiome, identifying metabolic complementarity between microbes, as well as the importance of symbionts present in low abundance. We also mined the metagenomes for putative viral sequences, highlighting the contribution of viruses to the overall metabolism of the sponge, and complement this data with metaproteomic sequencing to identify active metabolic pathways in both prokaryotes and viruses. This data now allows us to use I. basta as a model organism for studying host-microbe interactions and provides a basis for future (genomic) manipulative experiments.

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Project description:Marine sponges represent one of the few eukaryotic groups that ubiquitously harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of archaeal ammonia oxidizers (AOA). In this study, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and direct isotope-based functional assays. We demonstrate that the I. basta symbiont is not closely related to other genomically sequenced sponge AOA and is a member of a new genus. “Candidatus Nitrosospongia bastadiensis” is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Consistently, Ca N. bastadiensis encodes and expresses the genetic repertoire required for chemolithoautotrophic ammonia oxidation. Furthermore, we show that this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system likely involved in defense against foreign DNA, represent important adaptations of AOA to life within these ancient filter-feeding animals.

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