A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges

Cleary, Daniel F. R.; Oliveira, Vanessa; Gomes, Newton C.M.; Bialecki, A; Voogd, Nicole J. de

doi:10.1093/femsec/fiad014

Cited by 4 publications

References 76 publications

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Sponge-associated microbes in the twilight zone of Curaçao

Cleary,

van Bendegom,

Gomes

et al. 2024

Symbiosis

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Mesophotic reefs, located in the "Twilight Zone" of the ocean, are coral reefs that exist in relatively deep waters ranging from approximately 30 to 150 m below the surface. These reefs are situated just beyond the reach of conventional SCUBA diving and are typically explored using advanced diving techniques or with the aid of submersibles. In the present study, we used a state-of-the-art submersible to sample 26 sponge specimens belonging to 11 species. High (HMA) or low (LMA) microbial abundance status was assigned to species based on TEM imagery. Prokaryotic communities associated with these sponges were, furthermore, assessed using high-throughput sequencing. Proteobacteria, Chloroflexi, Actinobacteriota, and Acidobacteriota were the most abundant phyla overall. HMA/LMA status proved to be a highly significant predictor of prokaryotic composition. HMA sponges also tended to be more diverse in terms of richness and evenness than LMA sponges. 14 predictor-classes were identified using an exploratory technique based on machine learning including classes within the phyla Chloroflexi (e.g., Dehalococcoidia and JG30-KF-CM66) and Acidobacteriota (Thermoanaerobaculia and Subgroups 11 and 21). Previous studies have demonstrated the prevalence of the HMA/LMA dichotomy in shallow waters and, recently, the deep sea. Our results demonstrate its prevalence in the mesophotic realm.

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Sponge-associated microbes in the twilight zone of Curaçao

Cleary,

van Bendegom,

Gomes

et al. 2024

Symbiosis

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The impact of space, host dissimilitude, and environment on prokaryotic communities of golf ball sponges

Cleary,

de Voogd

2024

Marine Ecology

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Golf ball sponges are small, sometimes inconspicuous, sponges. They can be found across a range of habitats varying from perturbed and pristine coral reefs to harbours and marine lakes and from the deep sea to shallow waters. They can be difficult to distinguish in the field and have presented some problems with taxonomists lumping and splitting species due to the difficulty in defining clear species boundaries. In the present study, we sampled golf ball sponges from Indo‐Pacific and Caribbean locations and used 16S gene amplicon sequencing to study their prokaryotic communities. We show that golf ball sponges harbour a wide variety of prokaryotic communities. Among the most prevalent operational taxonomic units (OTUs), several belonged to a range of taxa, including the bacterial AqS1 and EC94 groups, which have been associated with genes known to facilitate interactions between hosts and microbes. Certain host taxa were enriched with OTUs classified to the SAR202 clade of Chloroflexi. Our findings show that prokaryotic dissimilarity varied as a function of space (geographical distance) and host dissimilitude. The importance of space and host dissimilitude, however, varied depending on the data transformation with host dissimilitude a more important predictor of untransformed data whereas space was a more important predictor of log‐transformed data. Given that log‐transformation downscales the influence of abundant taxa, we interpret these results by the tendency of closely related host organisms to host similar sets of abundant symbiotic microorganisms; distantly sampled specimens, in contrast, tend to harbour less abundant prokaryotic microorganisms found in the surrounding environment (e.g., seawater or sediment).

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The impact of space, host dissimilitude and environment on prokaryotic communities of golf ball sponges

Cleary,

de Voogd

2023

Preprint

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Golf ball sponges are small, sometimes inconspicuous, sponges. They can be found across a range of habitats varying from perturbed and pristine coral reefs to harbours and marine lakes and from the deep sea to shallow waters. They can be difficult to distinguish in the field and have presented some problems with taxonomists lumping and splitting species due to the difficulty in defining clear species traits. In the present study, we sampled golf ball sponges from Indo-Pacific and Caribbean locations and used 16S gene amplicon sequencing to study their prokaryotic communities. We show that golf ball sponges harbour a wide variety of prokaryotic communities. Among the most prevalent operational taxonomic units (OTUs), several belonged to a range of taxa, including AqS1 and ED94, which have been associated with genes known to facilitate interactions between hosts and microbes. Certain host taxa were enriched with OTUs assigned to the SAR202 clade of Chloroflexi. Our findings show that prokaryotic dissimilarity varied as a function of space (geographical distance) and host dissimilitude. The importance of space and host dissimilitude, however, varied depending on the data transformation with host dissimilitude a more important predictor of untransformed data whereas space was a more important predictor of log-transformed data. Given that log-transformation down scales the influence of abundant taxa, we interpret these results by the tendency of closely related host organisms to host similar abundant symbiotic microorganisms whereas specimens that are distantly sampled tend to harbour less abundant prokaryotic microorganisms that mirror the characteristics of their distant environments.

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A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges

Cited by 4 publications

References 76 publications

Sponge-associated microbes in the twilight zone of Curaçao

Sponge-associated microbes in the twilight zone of Curaçao

The impact of space, host dissimilitude, and environment on prokaryotic communities of golf ball sponges

The impact of space, host dissimilitude and environment on prokaryotic communities of golf ball sponges

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