Erratum to: The sponge microbiome project

Moitinho‐Silva, Lucas; Nielsen, Shaun; Almasi‐Hashiani, Amir; González, Antonio G.; Ackermann, Gail; Cerrano, Carlo; Astudillo‐García, Carmen; Easson, Cole G.; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Georgios; McCormack, Grace P.; Gao, Feng; Bell, James J.; Vicente, Jan; Björk, Johannes; Montoya, José M.; Olson, Julie B.; Réveillaud, Julie; Steindler, Laura; Pineda, Mari Carmen; Marra, Maria V.; Ilan, Micha; Taylor, Michael W.; Polymenakou, Paraskevi N.; Erwin, Patrick M.; Schupp, Peter J.; Simister, Rachel L.; Knight, Rob; Thacker, Robert; Costa, Rodrigo; Hill, Russell T.; López‐Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S.; Thomas, Torsten

doi:10.1093/gigascience/giy145

Cited by 3 publications

(4 citation statements)

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“…With its RED value of 0.87 ( Table 1 ), MAG B01 should represent a new genus. Global distribution analysis against the SMP database (Moitinho-Silva et al, 2017b ) revealed that the V4 region of the 16S rRNA gene in MAG B01 showed 100% identity with amplicons from three glass sponge individuals in the family Dactylocalycidae ( Figure 4 ), with relative abundances of 23.25, 8.78, and 8.60% in the respective communities ( Supplementary Table 5 ). B01 also shared 97–99% identities with sponge symbionts in three other sponge species, Aphrocallistes beatrix, Axinella sp., and an unnamed species, but was only 96% similar to its closest relatives from seawater samples ( Supplementary Table 5 ).…”

Section: Resultsmentioning

confidence: 99%

“…Finally, the remaining reads were subjected to coverM v0.2.0 ( https://github.com/wwood/CoverM ) to calculate the relative abundance of sponge-associated MAGs. To investigate the global distribution of a sponge symbiont, the V4 region of the 16S rRNA gene extracted from the MAG was searched by BLASTN (e-value cutoff: 1e-05) against the datasets of 16S rRNA gene sequences in the Sponge Microbiome Project (SMP) (Moitinho-Silva et al, 2017b ) and the Deep-sea Sponge Microbiome Project database (D-SMP) (Busch et al, 2022 ). Target sequences with >96% identity were retained to calculate their relative abundance in respective sponges.…”

Section: Methodsmentioning

confidence: 99%

“…Sponges usually harbor dense and diverse prokaryotic communities, which can account for up to 35% of the sponge biomass (Webster and Thomas, 2016 ; Pita et al, 2018 ). In terms of taxonomic diversity, up to 63 prokaryotic phyla have been recovered from marine sponges (Schmitt et al, 2012 ; Moitinho-Silva et al, 2017b ). Considering the diversity and potential functional importance of the symbiotic microbiome, sponges are frequently referred to “holobionts”, a complex and interdependent consortium that comprises the sponge host and the entire microbiome (Pita et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

Wei

Gao²,

Gong³

et al. 2023

Front. Microbiol.

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Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR–Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

Wei

Gao²,

Gong³

et al. 2023

Front. Microbiol.

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show abstract

“…This concept has however further room for improvement, as many biosynthetic pathways, involved genes, and the role of microbial symbionts are often not thoroughly understood yet, and might help to further comprehend the complex distribution patterns and evolution of secondary metabolites among sponge clades [ 212 ]. Investigations of the sponge microbiome have shown that microbial associations in sponges are to a large extent species specific [ 213 , 214 , 215 ]. Knowing the associated microbiome, potential function, and biosynthetic potential might help to identify if compounds are likely of microbial origin or produced by the sponge host [ 216 ].…”

Section: The Legacy Of Chemosystematics–perspectives On Phylogenetics and Biochemistrymentioning

confidence: 99%

A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution

et al. 2021

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Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.

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Bioinformatics for sperm phenotypic abnormalities:current situation and future trends

Zhang¹,

Zhan²,

Wang³

et al. 2022

Sci. Sin.-Vitae

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Erratum to: The sponge microbiome project

Cited by 3 publications

References 0 publications

Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution

Bioinformatics for sperm phenotypic abnormalities:current situation and future trends

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