| 1. |
- Steffen, Karin, 1989-, et al.
(författare)
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Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges
- 2022
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Ingår i: Scientific Reports. - : NATURE RESEARCH. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5 % of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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| 2. |
- Steffen, Karin, 1989-, et al.
(författare)
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Sea for yourself: evaluating the ddRADseq Stacks de novo pipeline with a reference genome in the deep-sea sponge Geodia barretti
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Reduced representation sequencing appraches such as ddRADseq allow to assess population connectivity and infer population summary statistics, both with and without a reference genome. However, as ddRADseq employs total DNA indiscriminate of the origin, the method warrants validation prior to application in microbial rich systems. One example of a complex system are sponges such as the North Atlantic high microbial abundance sponge Geodia barretti. This species is known to maintain large, putatively disjoint populations across the deep-sea, but its dispersal capabilities remain unclear as larvae have never been observed. To study the effect of microbial contamination on data processing and population genetic inference in ddRADseq, we produced a reference genome of G. barretti and collected 163 individuals across its habitat range and bathymetry (35–1560 m) in the North Atlantic. We processed the data with Stacks2 both with and without a reference genome (de novo and hybrid/‘reference-integrated’ approach). We found that strong population structures are recovered by both approaches and across different population genetic analyses (fastStructure, PCA, FST). Compared to previous work using microsatellites in shallow populations, we found only very weak population structure across large geographic stretches (>1000 km). However, over a third (34%) of the final loci produced by the de novo pipeline did not map to the reference genome indicating that these might be of microbial origin. For comparably complex systems this means that de novo RRS genotyping approaches may contain a considerable amount of off-target loci potentially biasing the results.
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| 3. |
- Taboada, Sergi, et al.
(författare)
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Long distance dispersal and oceanographic fronts shape the connectivity of the keystone sponge Phakellia ventilabrum in the deep northeast Atlantic
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about dispersal in deep-sea ecosystems, especially for sponges, which are abundant ecosystem engineers. Understanding patterns of gene flow in deep-sea sponges is essential, especially in areas where rising pressure from anthropogenic activities makes difficult to combine management and conservation. Here, we combined population genomics and oceanographic modelling to understand how Northeast Atlantic populations (Cantabrian Sea to Norway) of the deep-sea sponge Phakellia ventilabrum are connected. The analysis comprised ddRADseq derived SNP datasets of 166 individuals collected from 57 sampling stations from 17 different areas, including two Marine Protected Areas, one Special Area of Conservation and other areas with different levels of protection. The 4,017 neutral SNPs used indicated high connectivity and panmixis amongst the majority of areas (Ireland to Norway), spanning ca. 2,500-km at depths of 99-900 m. This was likely due to the presence of strong ocean currents allowing long-distance larval transport, as supported by our migration analysis and by 3D particle tracking modelling. On the contrary, the Cantabrian Sea and Roscoff (France) samples, the southernmost areas in our study, appeared disconnected from the remaining areas, probably due to prevailing current circulation patterns and topographic features, which might be acting as barriers for gene flow. Despite this major genetic break, our results suggest that all protected areas studied are well-connected with each other. Interestingly, analysis of SNPs under selection replicated results obtained for neutral SNPs. The relatively low genetic diversity observed along the study area, though, highlights the potential fragility of this species to changing climates, which might compromise resilience to future threats.
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| 4. |
- Wudrick, Alannah, et al.
(författare)
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A Pictorial Guide to the Epibenthic Megafauna of Orphan Knoll (northwest Atlantic) Identified from In Situ Benthic Video Footage
- 2020
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In 2010, Fisheries and Oceans Canada led a multidisciplinary oceanographic research mission onboard the Canadian Coast Guard Ship Hudson to the Northwest Atlantic Fisheries Organization Regulatory Area to collect benthic imagery and geological data in support of the identification of vulnerable marine ecosystems. Using the remotely operated vehicle ROPOS, six benthic video transects were collected on Orphan Knoll, a submerged circular continental fragment located 550 km northeast of St. John’s, Newfoundland. High-resolution video footage, digital still images, and specimen samples were collected between 1655 and 3004 m depth across the flanks and plateau of the knoll and Orphan Seamount. In 2007, the Northwest Atlantic Fisheries Organization implemented a ~15,800 km2 closure over Orphan Knoll to restrict the use of bottom- tending fishing gear in accordance with United Nations General Assembly Resolution 61/105. However, at the time, its benthic communities and the presence of vulnerable marine ecosystems had not been fully assessed. Here we present a pictorial guide to the epibenthic megafauna enumerated and taxonomically identified from five ROPOS transects collected on Orphan Knoll and Orphan Seamount. The purpose of this report is to provide a visual representation and taxonomic nomenclature scheme of the epibenthic megafauna of Orphan Knoll for use in future monitoring of the benthic communities of this unique topographic feature.
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