BUSCADOR RECOLECTA

This file contains data on number of mesopelagic fish collected during the CSIC-SUMMER survey carried out in October 2020 in five zones around the Iberian Peninsula: Balears and Alboran in the western Mediterranean, and Cadiz, Lisboa and Galicia. The scientific midwater trawl Mesopelagos fitted with a Multisampler placed at the end of the net was used to collect specimens at seven layers of the water column. The depth of the net was controlled by a SCANMAR system. In the five zones, hauls were carried out day and night to study vertical migration patterns of mesopelagic fish. A total of 24 deployments were made (between 0 and 700 m), of which 14 discriminated water layers. Additionally, to more accurately sample the epipelagic layers 7 night hauls were restricted to the first 210 m of the water column. Fish were identified and counted on board, or frozen for later processes in the laboratory. These data were obtained within the European Union Project 'Sustainable Management of Mesopelagic Resources' (SUMMER, Grant Agreement 817806) as funded by the Horizon 2020 Research and Innovation Programme, Horizon 2020 (H2020), grant/award no. 817806: Sustainable management of mesopelagic resources, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

Biofilm growth in porous media changes not only the hydrodynamic properties of the medium (reduction in porosity and permeability, and increase in dispersivity), but also the transport itself (breakthrough curves display increasingly fast first arrivals and long tails). These features are well reproduced by multicontinuum models (Multi-Rate Mass Transfer, MRMT) which can be used to describe reactive transport in heterogeneous porous media and facilitate the simulation of reactions that are localized within biofilms. Here, we present a conceptual and numerical model of biochemical reactive transport with dynamic biofilm growth based on MRMT formulations. Mass exchange between mobile water and immobile biofilm aggregates is represented by a memory function, which simplifies definition of MRMT parameters. We successfully tested this model on two sets of laboratory data and found that (a) a basic model based on the growth of uniformly sized biofilm aggregates fails to reproduce laboratory tracer tests and rate of biofilm growth, while a fractal growth model, which we obtain by integrating the memory functions of biofilm aggregates with a power law distribution, does; (b) the biofilm memory function evolves as the biofilm grows; and (c) the early time portion of eluted volume tracer breakthrough curves are independent of flow rate, whereas the tail becomes heavier when the flow rate is decreased, which implies that both advection controlled and diffusion controlled mass exchange coexist in biofilms. These findings imply that porous media biofilms are essentially different from those developing in human tissues or open spaces., The authors acknowledge the financial support of projects RESTORA (Agència Catalana de l'Aigua, ACA210/18/0040), ConMimo (Spanish Research Agency, AEI, number TED2021-131188B-C31), and Ciencia de Frontera CONAHCYT CF-2023-G-904. Additional funding was obtained from the Generalitat de Catalunya (2017 SGR1485) and the Spanish Ministry of Science and Innovation (Center of Excellence Severo-Ochoa, CSIC-IDAEA, CEX2018-000794-S). Financial support from National Natural Science Foundation of China (Grant 42307271) is acknowledged. J. W. is also sponsored by Shanghai Pujiang Program (Grant 23PJ1413200). We thank two anonymous reviewers for their approval and constructive comments that significantly helped improve the manuscript., Peer reviewed

EK80 raw data were collected during the 2020 SUMMER (Sustainable Management of Mesopelagic Resources) Mediterranean cruise (30 September 2020 to 18 October 2020) carried out by RV Sarmiento de Gamboa. Five frequencies (18, 38, 70, 120, 200 kHz) were operated on continuous wave (CW) mode with specific settings by the hull-mounted EK80. A maximum volume of 100 MB of individual raw file was used. The recording depths for 5 frequencies from 18 to 200 kHz were 1000, 1000, 750, 500, and 200 m. The transmitted power for 5 frequencies from 18 to 200 kHz were set to 2000, 1000, 750, 250 and 150 W. Calibrations were carried out on the 1st of October 2020 using a 33 mm tungsten sphere, and the calibration results were applied to the EK80. Raw power (W), number of transducer segments and transceiver impedance (Ohm) were stored in raw proprietary Simrad format (.raw, .idx). The raw files were all recorded according to the UTC+00:00 time zone, Horizon 2020 (H2020), grant/award no. 817806: Sustainable management of mesopelagic resources, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

Boscalid (2-Chloro-N-(4'-chlorobiphenyl-2-yl) nicotinamide), a pyridine carboxamide fungicide, is an inhibitor of the complex II of the respiration chain in fungal mitochondria. As boscalid is only moderately toxic for aquatic organisms (LC50 > 1-10 mg/L), current environmental levels of this compound in aquatic ecosystems, in the range of ng/L-μg/L, are considered safe for aquatic organisms. In this study, we have exposed zebrafish (Danio rerio), Japanese medaka (Oryzias latipes) and Daphnia magna to a range of concentrations of boscalid (1-1000 μg/L) for 24 h, and the effects on heart rate (HR), basal locomotor activity (BLA), visual motor response (VMR), startle response (SR), and habituation (HB) to a series of vibrational or light stimuli have been evaluated. Moreover, changes in the profile of the main neurotransmitters have been determined. Boscalid altered HR in a concentration-dependent manner, leading to a positive or negative chronotropic effect in fish and D. magna, respectively. While boscalid decreased BLA and increased VMR in Daphnia, these behaviors were not altered in fish. For SR and HB, the response was more species- and concentration-specific, with Daphnia exhibiting the highest sensitivity. At the neurotransmission level, boscalid exposure decreased the levels of L-aspartic acid in fish larvae and increased the levels of dopaminergic metabolites in D. magna. Our study demonstrates that exposure to environmental levels of boscalid alters cardiac activity, impairs ecologically relevant behaviors, and leads to changes in different neurotransmitter systems in phylogenetically distinct vertebrate and invertebrate models. Thus, the results presented emphasize the need to review the current regulation of this fungicide., Peer reviewed

Supplementary Table 1. Epithelial and mesenchymal genes. List of epithelial and mesenchymal genes extracted from refs. 12,55. Supplementary Table 2. BC-PINGs signature. Supplementary Table 3. Gene symbols and names. Supplementary Table 4. List of antibodies used for immunofluorescence and western blot analyses. Supplementary Table 5. List of oligonucleotides used for RT–qPCR and genotyping. Supplementary Table 6. Workflow in kidney and cancer sample single-cell analyses. Supplementary Table 7. List of TF binding motifs identified by SCENIC analysis., Peer reviewed

Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures., We acknowledge the help of Pere Joan Gelabert in obtaining topographical and vegetation data of watersheds using ArcMap., Peer reviewed

Datasets listed in this bundled publication: - Yang, Y.; Proud, R.; Castellón, A. et al. (2023): Acoustic data collected by wideband autonomous transceiver (WBAT, 35 to 445 kHz) during RV Sarmiento de Gamboa cruise 'Sustainable Management of Mesopelagic Resources' (SUMMER) in 2020 to the Mediterranean. https://doi.org/10.1594/PANGAEA.938194 - Yang, Y.; Proud, R.; Castellón, A. et al. (2023): EK80 raw broadband (18, 35 to 260 kHz) stationary observations during RV Sarmiento de Gamboa cruise 'Sustainable Management of Mesopelagic Resources' (SUMMER) in 2020 to the Mediterranean. https://doi.org/10.1594/PANGAEA.938510 - Yang, Y.; Proud, R.; Castellón, A. et al. (2023): EK80 raw multi-frequency (18, 38, 70, 120, 200 kHz) acoustic data collected during RV Sarmiento de Gamboa cruise 'Sustainable Management of Mesopelagic Resources' (SUMMER) in 2020 to the Mediterranean. https://doi.org/10.1594/PANGAEA.938688, These data consist of both underway and station echosounder observations collected during the 2020 SUMMER (Sustainable Management of Mesopelagic Resources) Mediterranean cruise (30 September 2020 to 18 October 2020) on the RV Sarmiento de Gamboa. Narrowband (18, 38, 70, 120, 200 kHz) underway acoustic data were collected continuously using hull-mounted Simrad EK80 echosounders. The recording depths for the 5 frequencies were 1000, 1000, 750, 500, and 200 m respectively. Calibrations were carried out on the 1st of October 2020 using a 33 mm tungsten sphere,and the calibration results were applied to the instruments. During the survey, a Simrad wideband autonomous receiver (WBAT) was deployed down to a depth of 500 m whilst on station. In total, 31 drops were carried out at 5 stations. Four transducers (central frequencies were 45, 120, 200, 333 kHz) were operated using the WBAT in frequency modulated (FM) mode (bandwidth ranging from 45 to 445 kHz). The WBAT calibration data were collected using a 33 mm tungsten sphere. During the deployment of the WBAT, the hull-mounted EK80 was switched to FM mode to record broadband measurements. Raw power (W), number of transducer segments and transceiver impedance (Ohm) were stored in raw proprietary Simrad format (.raw, .idx), Horizon 2020 (H2020), grant/award no. 817806: Sustainable management of mesopelagic resources, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

In recent years, instrumental improvements have enabled the spread of mass spectrometry-based lipidomics platforms in biomedical research. In mass spectrometry, the reliability of generated data varies for each compound, contingent on, among other factors, the availability of labeled internal standards. It is challenging to evaluate the data for lipids without specific labeled internal standards, especially when dozens to hundreds of lipids are measured simultaneously. Thus, evaluation of the performance of these platforms at the individual lipid level in interlaboratory studies is generally not feasible in a time-effective manner. Herein, using a focused subset of sphingolipids, we present an in-house validation methodology for individual lipid reliability assessment, tailored to the statistical analysis to be applied. Moreover, this approach enables the evaluation of various methodological aspects, including discerning coelutions sharing identical selected reaction monitoring transitions, pinpointing optimal labeled internal standards and their concentrations, and evaluating different extraction techniques. While the full validation according to analytical guidelines for all lipids included in a lipidomics method is currently not possible, this process shows areas to focus on for subsequent method development iterations as well as the robustness of data generated across diverse methodologies., Open access funding provided by Karolinska Institute. CEW received support from the Swedish Heart and Lung Foundation (HLF 20230463 and HLF 20210519) and the Swedish Research Council (2022-00796). BZ is supported by the H2020 ITN consortium ArthritisHeal (#812890), the Konung Gustaf V:s 80-årsfond (FAI-2020-0732), and the Swedish Heart and Lung Foundation (HLF20230363). AW received support from the Swedish Heart and Lung Foundation (HLF 20190017) and the Swedish Research Council (2018-00520). JJ received support from the Spanish Ministry of Science and Innovation MCIU/AEI/10.13039/501100011033 and Severo Ochoa Excelencia Grant CEX2018-000794-S., Peer reviewed

Figure S1. No differences in body weight, gross cerebellar architecture, and motorcoordination between wild-type and GluK4 KO mice, Related to Figures 1 and 2. -- Figure S2. Basic CF- and PF-EPSC properties in wild-type and GluK4 KO mice, Related to Figure 1. -- Figure S3. The KAR components are absent in CF-EPSCs of GluK1 KO and GluK4 KO mice, and CF-EPSCs are reduced in PC-specific GluK4 KO mice, Related to Figure 1. -- Figure S4. The GluK1 KO cerebellum exhibited a reduction in CFPC synapses, Related to Figure 3. -- Figure S5. PF/ΔV-stim failed to induce LTD in C1ql1 KO and Bai3 KO PCs, Related to Figure 2. -- Figure S6. Mono CF innervation to single PC in adult GluK4 KO mice. -- Figure S7. MAP allows immunodetection of endogenous GluK4 at CFPC synapse. -- Figure S8. GluK4 and C1ql1 signals on vGluT2-positive area in GluK4 KO, C1ql1 KO and Bai3 KO mice. -- Figure S9. C1ql1 binds to the ATD of GluK4 but not GluK1 in vitro. -- Figure S10. The ATD of GluK4 indirectly binds to Bai3 via C1ql1 in vitro. -- Figure S11. KAR-mediated currents in GluK4 KO PCs expressing HA-GluK4. -- Figure S12. No KAR component at PF-EPSCs in GluK4 KO PCs overexpressing GluK4. -- Figure S13. Transduction efficiency of PCs by retro-orbital injection of AAV(PHP.eB. -- Figure S14. A proposed model illustrating the KAR−C1ql1−Bai3 complex on CF−PC synapses for synaptic integrity, LTD and motor learning, Peer reviewed

Supplemental figures and table - spectrum.00254-24-s0001.doc Fig. S1-S5; Table S7., Tables S8 and S9 - spectrum.00254-24-s0002.xlsx Table S8: Klebsiella phages isolated in K. pneumoniae clinical isolates. Table S9: Functional annotation of Klebsiella phages., Supplemental tables - spectrum.00254-24-s0003.xlsx Tables S1, S3, S5, and S6., Table S2 - spectrum.00254-24-s0004.xlsx Table S2: Functional annotation of Klebsiella phages., Table S4 - spectrum.00254-24-s0005.docx Table S4: Amino acid sequences of detected depolymerase proteins., Peer reviewed