Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: April 8, 2024

Abstract Background Most researches on sponge holobionts focus primarily symbiotic microbes, yet data at the level of hologenome are still relatively scarce. Understanding host and its microbial gene expression profiles host-microbes interplay in different niches represents a key aspect hologenome. Using Hawaiian demosponge Mycale grandis as model, i.e. rocks, surface coral Porites compressa , under alga Gracilaria salicornia we compared bacterial fungal community structure, functional diversity, pattern transcriptome by integrating open-format (deep sequencing) closed-format (GeoChip microarray) high-throughput techniques. Results Little inter-niche variation phylogenetic diversity was detected for M. niches, but clear niche-dependent variability microbiota uncovered GeoChip microarray analyses. Particularly, genes related to innate immunity recognition showed strong correlation with symbionts’ transcriptional richness niches. The cross-niche respect symbiont holobiont putatively reflects niche-specific selective pressure diversity. Conclusions Niche–dependent were suggested though little detected, particularly found be closely microbes. Altogether, these findings provide novel insights into black box one level.

Language: Английский

A novel target‐enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 27, 2023

Abstract With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation management efforts. Marine sponges are species‐rich ecological key players on coral reefs, but still poorly understood. This particularly true the demosponge order Haplosclerida, whose systematic contentious due to incongruencies between morphological molecular phylogenetic hypotheses. The single gene markers applied in previous studies did not resolve these discrepancies. Hence, there high need genome‐wide approach derive phylogenetically robust classification understand this group's evolutionary relationships. To end, we developed target enrichment‐based multilocus probe assay Haplosclerida using transcriptomic data. consists 20,000 enrichment probes targeting 2956 ultraconserved elements coding (i.e. exon) regions across genome was tested 26 haplosclerid specimens from Red Sea. Our target‐enrichment correctly placed our samples well‐supported phylogeny, agreement with phylogenies. results demonstrate applicability high‐resolution genomic methods systematically complex marine invertebrate group provide promising phylogenies Haplosclerida. Subsequently, will lead biologically unambiguous taxonomic revisions, interpretations biological observations new avenues research, managing diversity.

Language: Английский

rRNA depletion for holobiont metatranscriptome profiling across demosponges

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Aug. 14, 2022

Abstract Despite the extensive knowledge of sponge microbiome diversity, a critical gap persists concerning molecular mechanisms that govern host-symbiont interactions. Deciphering these is crucial for understanding how holobionts respond to environmental changes and identifying potential disruptions in sponge-microbe associations. A hindrance progress characterizing crosstalk scarcity broadly applicable methods efficiently sequencing meta-transcriptomes across diverse array species. To tackle this challenge, we have introduced hybrid-capture strategy capable selectively depleting bacterial rRNA from total RNA extracts obtained highly divergent demosponges with varying complexities. Our innovative pan-demosponge depletion approach streamlines efficient characterization metatranscriptomes within demosponge holobionts, concurrently facilitating quantification gene expression both host its microbiome. This methodological advancement represents significant stride unraveling intricacies interactions, providing robust platform future investigations broad spectrum

Language: Английский