ALBERT

Description: Onboard, cephalopods were identified morphologically to the lowest taxonomic level possible (species, genus or family), and whole specimens were preserved in formalin as voucher. In addition, tissue samples of some specimen were collected and preserved in ethanol for barcoding and the genetic reference database used for eDNA metabarcoding.

Description: Net catches of cephalopods were obtained during the cruises POS320/2 (March 2005), MSM49 (November/December 2015) and WH383 (March/April 2015) off Cabo Verde at a total of 18 stations at depths between 0 and 1000 m. Cephalopods were caught during POS320/2 with either a Isaacs-Kidd midwater trawl (IKMT) with a 6 m2 net opening, 4 mm mesh size equipped with a flowmeter, a Hydro-Bios Multinet Maxi with a 0.5 m2 net opening and 500 µm mesh size between the surface and 250 m water depth, or an 80 feet bottom trawl. Net sampling during MSM49 was conducted with two types of multiple opening/closing nets (MOCNESS) and an IKMT. The smaller MOCNESS had a net opening of 1 m2 opening (three nets with a mesh size of 2 mm and six nets with a mesh size of 335 μm) and the larger MOCNESS a net opening of 10 m2 opening (five nets, mesh size: 1.5 mm) and were deployed between the surface to 1000 m. The IKMT had a net opening of 7 m2 and ended in a cod end of 500 µm mesh size. It was deployed to a maximum depth of 500 m. During WH383 a pelagic trawl ('Aalnetz', Engel Netze, Bremerhaven, Germany) with a mouth opening of 16 x 30 m, length of 150 m including multiple opening-closing device, 260 meshes by 180 cm stretched mesh size at the front, a cod end 20 mm stretched mesh-opening and a 1.8 mm inlet sewn into last 1 m of cod end was used with a multisampler (Construction Services AS, Bergen, Norway) allowing depth-stratified sampling. During WH383 three strata (mean vertical extension of ca. 40 m) were trawled mostly during night and one time during daytime at depths between 30 and 700 m in horizontal tows for 30 minutes per stratum with a mean speed of three knots (2.8-3.3 kn). During this cruise, night trawls took place at 22:00 local time, and the day-time trawl at 12:00 local time. Onboard, cephalopods were identified morphologically to the lowest taxonomic level possible (species, genus or family), and whole specimens were preserved in formalin as voucher. In addition, tissue samples of some specimen were collected and preserved in ethanol for barcoding and the genetic reference database used for eDNA metabarcoding. Pelagic video transects with the Pelagic In-Situ Observation System (PELAGIOS, (Hoving et al., 2019a)) were conducted during the cruises MSM49 (Christiansen et al., 2016) (transects between 30 and 1000 m, total towing duration 〉 80h), MSM61 (Fiedler et al., 2020) (transects between 80 and 1200 m, total hours of observations 〉 32h), POS520 (Hoving et al., 2018, p. 520) (transects between 30 and 2500 m, total hours of observations 27h), POS532 (Hoving et al., 2019b) (transects between 30 and 990 m, total hours of observations 19h) and M119 (Brandt, 2016) (transects between 50 and 700 m, total hours of observations 〉 20h) between 2015 and 2019 (Figure 1). PELAGIOS is a battery powered, high-definition camera system that is towed horizontally via a single-wired conductive sea-cable at 0.5 m s -1. Around 0.45 m2 of the water column in front of the camera is illuminated with an LED array. The attached depth sensor and/or a sensor for conductivity, temperature and depth (CTD) with oxygen sensor allows for hydrographic measurements and depth monitoring during transects. Pelagic video transects were conducted between 11-33 minutes per depth, towing the camera horizontally at specified depths. A deep-sea telemetry system allows for transmission of a low-resolution preview of the recorded video. During the cruises POS520 and POS532 the manned submersible JAGO (GEOMAR, Helmholtz Centre for Ocean Research) was used for 30 deployments of about four hours each between the surface and 350 m water depth. During the dives, video was recorded by a high-resolution camera. The videos taken during the PELAGIOS and JAGO dives were annotated manually using the Video Annotation and Reference System (VARS) developed at the Monterey Bay Aquarium Research Institute, which allows annotation and congruent collection of video frames. We also provide raw data on environmental DNA samples taken during POS532 in February 2019 at five stations. The stations off the islands Santo Antão and Fogo were close to the coast (maximum sampled depth 2500 m), CVOO was a reference station in the open ocean (maximum sampled depth 3000 m) and the stations Cyclone and Anticyclone were located eddies that had formed in the wake of Fogo and had propagated southwards (maximum sampled depths 2200 and 600 m, respectively). Per sampled depth, three biological replicates of two liters of seawater each were collected from three different 10 liter Niskin bottles mounted on a CTD rosette. For filtration, 0.22 µm pore size Sterivex-GP filter (Merck Millipore) were directly connected to the Niskin bottle with sterile tubing. The weight of the water in the Niskin bottles was sufficient to filter two liters of seawater per filter. The filters were closed with sterile plastic caps and stored at -80°C until further processing in the laboratory.

Description: Net catches of cephalopods were obtained during the cruises POS320/2 (March 2005), MSM49 (November/December 2015) and WH383 (March/April 2015) off Cabo Verde at a total of 18 stations at depths between 0 and 1000 m. Cephalopods were caught during POS320/2 with either a Isaacs-Kidd midwater trawl (IKMT) with a 6 m2 net opening, 4 mm mesh size equipped with a flowmeter, a Hydro-Bios Multinet Maxi with a 0.5 m2 net opening and 500 µm mesh size between the surface and 250 m water depth, or an 80 feet bottom trawl. Net sampling during MSM49 was conducted with two types of multiple opening/closing nets (MOCNESS) and an IKMT. The smaller MOCNESS had a net opening of 1 m2 opening (three nets with a mesh size of 2 mm and six nets with a mesh size of 335 μm) and the larger MOCNESS a net opening of 10 m2 opening (five nets, mesh size: 1.5 mm) and were deployed between the surface to 1000 m. The IKMT had a net opening of 7 m2 and ended in a cod end of 500 µm mesh size. It was deployed to a maximum depth of 500 m. During WH383 a pelagic trawl ('Aalnetz', Engel Netze, Bremerhaven, Germany) with a mouth opening of 16 x 30 m, length of 150 m including multiple opening-closing device, 260 meshes by 180 cm stretched mesh size at the front, a cod end 20 mm stretched mesh-opening and a 1.8 mm inlet sewn into last 1 m of cod end was used with a multisampler (Construction Services AS, Bergen, Norway) allowing depth-stratified sampling. During WH383 three strata (mean vertical extension of ca. 40 m) were trawled mostly during night and one time during daytime at depths between 30 and 700 m in horizontal tows for 30 minutes per stratum with a mean speed of three knots (2.8-3.3 kn). During this cruise, night trawls took place at 22:00 local time, and the day-time trawl at 12:00 local time. Onboard, cephalopods were identified morphologically to the lowest taxonomic level possible (species, genus or family), and whole specimens were preserved in formalin as voucher.

Description: Fundamental insight on predator-prey dynamics in the deep sea is hampered by a lack of combined data on hunting behavior and prey spectra. Deep-sea niche segregation may evolve when predators target specific prey communities, but this hypothesis remains untested. We combined environmental DNA (eDNA) metabarcoding with biologging to assess cephalopod community composition in the deep-sea foraging habitat of two top predator cetaceans. Here, we are presenting the eDNA data from seawater samples obtained during a cruise on RV Pelagia in 2018 off Terceira, Azores, sampled directly in the foraging habitats of two cetacean top-predators from the surface to 1600 m. The water was collected using Niskin bottles mounted on a CTD rosette at seven or eight depths in biological triplicates and filtered on sterile Sterivex filter. After DNA extraction and PCR amplification with two universal cephalopod primer (Ceph18S, targeting the nuclear 18S rRNA gene and CephMLS targeting the mitochondrial 16S rRNA gene), the samples were sequenced on an Illumina MiSeq with the MiSeq Reagent kit v3 (600 cycles).

Description: Pelagic video transects with the Pelagic In-Situ Observation System (PELAGIOS, (Hoving et al., 2019a)) were conducted during the cruises MSM49 (Christiansen et al., 2016) (transects between 30 and 1000 m, total towing duration 〉 80h), MSM61 (Fiedler et al., 2020) (transects between 80 and 1200 m, total hours of observations 〉 32h), POS520 (Hoving et al., 2018, p. 520) (transects between 30 and 2500 m, total hours of observations 27h), POS532 (Hoving et al., 2019b) (transects between 30 and 990 m, total hours of observations 19h) and M119 (Brandt, 2016) (transects between 50 and 700 m, total hours of observations 〉 20h) between 2015 and 2019 (Figure 1). PELAGIOS is a battery powered, high-definition camera system that is towed horizontally via a single-wired conductive sea-cable at 0.5 m s -1. Around 0.45 m2 of the water column in front of the camera is illuminated with an LED array. The attached depth sensor and/or a sensor for conductivity, temperature and depth (CTD) with oxygen sensor allows for hydrographic measurements and depth monitoring during transects. Pelagic video transects were conducted between 11-33 minutes per depth, towing the camera horizontally at specified depths. A deep-sea telemetry system allows for transmission of a low-resolution preview of the recorded video. During the cruises POS520 and POS532 the manned submersible JAGO (GEOMAR, Helmholtz Centre for Ocean Research) was used for 30 deployments of about four hours each between the surface and 350 m water depth. During the dives, video was recorded by a high-resolution camera. The videos taken during the PELAGIOS and JAGO dives were annotated manually using the Video Annotation and Reference System (VARS) developed at the Monterey Bay Aquarium Research Institute, which allows annotation and congruent collection of video frames. We also provide raw data on environmental DNA samples taken during POS532 in February 2019 at five stations. The stations off the islands Santo Antão and Fogo were close to the coast (maximum sampled depth 2500 m), CVOO was a reference station in the open ocean (maximum sampled depth 3000 m) and the stations Cyclone and Anticyclone were located eddies that had formed in the wake of Fogo and had propagated southwards (maximum sampled depths 2200 and 600 m, respectively). Per sampled depth, three biological replicates of two liters of seawater each were collected from three different 10 liter Niskin bottles mounted on a CTD rosette. For filtration, 0.22 µm pore size Sterivex-GP filter (Merck Millipore) were directly connected to the Niskin bottle with sterile tubing. The weight of the water in the Niskin bottles was sufficient to filter two liters of seawater per filter. The filters were closed with sterile plastic caps and stored at -80°C until further processing in the laboratory.

Description: Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B’s preference for psbA, suggesting that there are other determinants of specificity in vivo.

Description: Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.

Description: The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.