ALBERT

Description: Deep-sea sponge grounds are underexplored ecosystems that provide numerous goods and services to the functioning of the deep-sea. This study assessed the microbial diversity (by 16S rRNA gene amplicon sequencing) in embryos, juveniles and adults of Craniella zetlandica and Craniella infrequens, common and abundant representatives of deep-sea sponge grounds in the North Atlantic. For this study, in total 39 sponge individuals of the two sponge species were collected and analysed for their associated microbial community composition: C. zetlandica (8 adults, of which one was brooding, and 9 juveniles) and C. infrequens (8 adults, of which four were brooding, and 9 juveniles). We use the term 'juvenile' for small (i.e. mean diameter = 1 cm for C. infrequens; and maximal diameter = 0.3 cm for C. zetlandica), young individuals. For C. zetlandica, juveniles were sampled in September 2018 from an aquarium system (Bergen, Norway). C. zetlandica juveniles were smaller (and most likely younger) than the in situ sampled C. infrequens juveniles and therefore flash-frozen as a whole. Embryos of both sponge species were carefully picked out of the parent sponges with sterile spring steel forceps onboard the research vessel using a stereomicroscope. Ten whole embryos were pooled per adult sponge to account for the small biomass. Data such as presented here provide information on the recruitment of deep-sea sponge holobionts which is needed to develop integrated management tools of such vulnerable marine ecosystems.

Description: Dataset contains metainformation to the samples used in the given pulication: links to Bioprojects, Biosamples, metagenome assemblies and raw data.

Description: Despite the development of several cultivation methods, the rate of discovery of microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating novel species in the laboratory. Furthermore, no current cultivation technique is capable of selectively isolating and cultivating specific bacterial taxa or phylogenetic groups independently of morphological or physiological properties. Here, we developed a new method to isolate living bacteria solely based on their 16S rRNA gene sequence. We showed that bacteria can survive a modified version of the standard fluorescence in situ hybridization (FISH) procedure, in which fixation is omitted and other factors, such as centrifugation and buffers, are optimized. We also demonstrated that labeled DNA probes can be introduced into living bacterial cells using chemical transformation and that specific hybridization occurs. This new method, which we call live-FISH, was then combined with fluorescence-activated cell sorting (FACS) to sort specific taxonomic groups of bacteria from mock and natural bacterial communities and subsequently culture them. Live-FISH represents the first attempt to systematically optimize conditions known to affect cell viability during FISH and then to sort bacterial cells surviving the procedure. No sophisticated probe design is required, making live-FISH a straightforward method to be potentially used in combination with other single-cell techniques and for the isolation and cultivation of new microorganisms.

Description: Video showing release of embryos (em) from a Craniella zetlandica specimen upon sampling by remotely operated vehicle at 225 m depth in Stjernsund, Northern Norway (70.2707 °N, 22.4778 °E). The footage was recorded on 2018-08-13 at 10:50 UTC by ROV Ægir (University of Bergen) during the research cruise GS2018108 onboard RV G.O. Sars (dive identifier GS2018108-78-ROV-52).

Description: Individuals of the breadcrumb sponge Halichondria panicea were collected from the field to perform phagocytic experiments. Collection site: coast of Schilksee (54.424278 N, 10.175794 E; Kiel, Germany) on August 7th 2022 at 8 am. Sponges were collected by carefully detaching them from crevices at 1-3 m depth by snorkeling. Name of the laboratory: H. panicea individuals were transported to the KIMMOCC climate chamber facilities at GEOMAR Helmholtz Centre for Ocean Research Kiel (Germany), where they were kept for two weeks under controlled temperature (room: 10°C; water: 17°C), and with water supplied from the Kiel Fjord. Culture conditions during the experiment: The phagocytic experiments started on Aug 15th 2022, and were performed in the aforementioned facilities of GEOMAR. All the experiments lasted for one week. The experiments consisted on incubating whole sponge individuals in natural seawater for 30 min with green microalgae (Nannochloropsis sp.; live culture purchased from BlueBio Tech (Germany)), live TAMRA-stained bacteria (isolate PP-XX7 ; 16S rRNA gene sequence similarity of 98.6 % with Vibrio sp. NBRC 101805 and 97.0% to Vibrio variabilis R-40492T),) or 1 µm fluorescent latex beads (Fluoresbrite YG microsphere, Cat. 17154-10, Polyscience). Water samples were taken at time intervals through the incubation period to estimate particle uptake (i.e., filtration) by the sponge using flow cytometry. Fluorescence-activated cell sorting (FACS) of sponge cells extracted from H. panciea tissue from the individuals used during the phagocytic experiment was used to quantify phagocytic activity (i.e., the population of sponge cells with internalized particles). Particle uptake of H. panicea individuals used during the phagocytic assays. Sponges were incubated for 30 min with three Nannochloropsis sp., TAMRA-stained bacteria (Vibrio sp.), or fluorescent latex beads (1 µm). Differenet algal concentration and chase periods were tested. Water samples for flow cytometry were taken at time intervals. Controls: seawater incubations. A linear or exponential model (seawater and sponge, respectively) was used to calculate the particle concentration at the start (C0) and at the end (C30) of the incubation. Particle uptake (C0-C30) was corrected based on the seawater control incubations. y = particle concentration; x = time; R2 = goodness of fit.

Description: Individuals of the breadcrumb sponge Halichondria panicea were collected from the field to perform phagocytic experiments. Collection site: coast of Schilksee (54.424278 N, 10.175794 E; Kiel, Germany) on August 7th 2022 at 8 am. Sponges were collected by carefully detaching them from crevices at 1-3 m depth by snorkeling. Name of the laboratory: H. panicea individuals were transported to the KIMMOCC climate chamber facilities at GEOMAR Helmholtz Centre for Ocean Research Kiel (Germany), where they were kept for two weeks under controlled temperature (room: 10°C; water: 17°C), and with water supplied from the Kiel Fjord. Culture conditions during the experiment: The phagocytic experiments started on Aug 15th 2022, and were performed in the aforementioned facilities of GEOMAR. All the experiments lasted for one week. The experiments consisted on incubating whole sponge individuals in natural seawater for 30 min with green microalgae (Nannochloropsis sp.; live culture purchased from BlueBio Tech (Germany)), live TAMRA-stained bacteria (isolate PP-XX7 ; 16S rRNA gene sequence similarity of 98.6 % with Vibrio sp. NBRC 101805 and 97.0% to Vibrio variabilis R-40492T),) or 1 µm fluorescent latex beads (Fluoresbrite YG microsphere, Cat. 17154-10, Polyscience). Water samples were taken at time intervals through the incubation period to estimate particle uptake (i.e., filtration) by the sponge using flow cytometry. Fluorescence-activated cell sorting (FACS) of sponge cells extracted from H. panciea tissue from the individuals used during the phagocytic experiment was used to quantify phagocytic activity (i.e., the population of sponge cells with internalized particles). FACS quantification of phagocytic sponge cells of H. panicea individuals used during the phagocytic assays. Sponges were incubated for 30 min with three Nannochloropsis sp., TAMRA-stained bacteria (Vibrio sp.), or fluorescent latex beads (1 µm). Differenet algal concentration and chase periods were tested. The sponge (host) cell suspension from each individual was run in the FACS three times (i.e., 3 technical replicates). The average number of events of the replicates is presented. Controls: individuals incubated without particle to correct for natural fluorescence in sponge cells. Bulk sponge cells: total DAPI-stained cell fraction; Non-phagocytic cells: cells without incorporated particle; Phagocytic cells: cells with incorporated particle.

Description: Individuals of the breadcrumb sponge Halichondria panicea were collected from the field to perform phagocytic experiments. Collection site: coast of Schilksee (54.424278 N, 10.175794 E; Kiel, Germany) on August 7th 2022 at 8 am. Sponges were collected by carefully detaching them from crevices at 1-3 m depth by snorkeling. Name of the laboratory: H. panicea individuals were transported to the KIMMOCC climate chamber facilities at GEOMAR Helmholtz Centre for Ocean Research Kiel (Germany), where they were kept for two weeks under controlled temperature (room: 10°C; water: 17°C), and with water supplied from the Kiel Fjord. Culture conditions during the experiment: The phagocytic experiments started on Aug 15th 2022, and were performed in the aforementioned facilities of GEOMAR. All the experiments lasted for one week. The experiments consisted on incubating whole sponge individuals in natural seawater for 30 min with green microalgae (Nannochloropsis sp.; live culture purchased from BlueBio Tech (Germany)), live TAMRA-stained bacteria (isolate PP-XX7 ; 16S rRNA gene sequence similarity of 98.6 % with Vibrio sp. NBRC 101805 and 97.0% to Vibrio variabilis R-40492T),) or 1 µm fluorescent latex beads (Fluoresbrite YG microsphere, Cat. 17154-10, Polyscience). Water samples were taken at time intervals through the incubation period to estimate particle uptake (i.e., filtration) by the sponge using flow cytometry. Fluorescence-activated cell sorting (FACS) of sponge cells extracted from H. panciea tissue from the individuals used during the phagocytic experiment was used to quantify phagocytic activity (i.e., the population of sponge cells with internalized particles).

Description: Until now few studies have explored the microbiomes of glass sponges (Hexactinellida). Vazella pourtalesii forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf. Using metagenomic binning we performed detailed analyses of the metabolic functional capacities of four V. pourtalesii-associated microbial taxa (SAR324, Patescibacteria, Nanoarchaeota, and Crenarchaeota).