Food determines ephemerous and non-stable gut microbiome communities in juvenile wild and farmed Mediterranean fish

Novel insights were provided by contrasting the composition of wild and farmed fish gut microbiomes because the latter had essentially different environmental conditions from those in the wild. This was reflected in the gut microbiome of the wild Sparus aurata and Xyrichtys novacula studied here, which showed highly diverse microbial community structures, dominated by Proteobacteria, mostly related to an aerobic or microaerophilic metabolism, but with some common shared major species, such as Ralstonia sp. On the other hand, farmed non-fasted S. aurata individuals had a microbial structure that mirrored the microbial composition of their food source, which was most likely anaerobic, since several members of the genus Lactobacillus, probably revived from the feed and enriched in the gut, dominated the communities. The most striking observation was that after a short fasting period (86 h), farmed gilthead seabream almost lost their whole gut microbiome, and the resident community associated with the mucosa had a very much reduced diversity that was highly dominated by a single potentially aerobic species Micrococcus sp., closely related to M. flavus. The results pointed to the fact that, at least for the juvenile S. aurata studied, most of the microbes in the gut were transient and highly dependent on the feed source, and that only after fasting for at least 2 days could the resident microbiome in the intestinal mucosa be determined. Since an important role of this transient microbiome in relation to fish metabolism could not be discarded, the methodological approach needs to be well designed in order not to bias the results. The results have important implications for fish gut studies that could explain the diversity and occasional contradictory results published in relation to the stability of marine fish gut microbiomes, and might provide important information for feed formulation in the aquaculture industry.info:eu-repo/semantics/publishedVersio

Automatic detection and classification of coastal Mediterranean fish from underwater images: Good practices for robust training

11 pages, 3 figures, 5 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2023.1151758/full#supplementary-material.-- Data availability statement: The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary MaterialFurther investigation is needed to improve the identification and classification of fish in underwater images using artificial intelligence, specifically deep learning. Questions that need to be explored include the importance of using diverse backgrounds, the effect of (not) labeling small fish on precision, the number of images needed for successful classification, and whether they should be randomly selected. To address these questions, a new labeled dataset was created with over 18,400 recorded Mediterranean fish from 20 species from over 1,600 underwater images with different backgrounds. Two state-of-the-art object detectors/classifiers, YOLOv5m and Faster RCNN, were compared for the detection of the ‘fish’ category in different datasets. YOLOv5m performed better and was thus selected for classifying an increasing number of species in six combinations of labeled datasets varying in background types, balanced or unbalanced number of fishes per background, number of labeled fish, and quality of labeling. Results showed that i) it is cost-efficient to work with a reduced labeled set (a few hundred labeled objects per category) if images are carefully selected, ii) the usefulness of the trained model for classifying unseen datasets improves with the use of different backgrounds in the training dataset, and iii) avoiding training with low-quality labels (e.g., small relative size or incomplete silhouettes) yields better classification metrics. These results and dataset will help select and label images in the most effective way to improve the use of deep learning in studying underwater organismsProject DEEP-ECOMAR. 10.13039/100018685-Comunitat Autonoma de les Illes Balears through the Direcció General de Política Universitària i Recerca with funds from the Tourist Stay Tax law ITS 2017-006 (Grant Number: PRD2018/26). [...] The present research was carried out within the framework of the activities of the Spanish Government through the “María de Maeztu Centre of Excellence” accreditation to IMEDEA (CSIC-UIB) (CEX2021-001198-M) and the “Severo Ochoa Centre Excellence” accreditation to ICM-CSIC (CEX2019-000928-S) and the Research Unit Tecnoterra (ICM-CSIC/UPC)Peer reviewe

Food determines ephemerous and non-stable gut microbiome communities in juvenile wild and farmed Mediterranean fish

Novel insights were provided by contrasting the composition of wild and farmed fish gut microbiomes because the latter had essentially different environmental conditions from those in the wild. This was reflected in the gut microbiome of the wild Sparus aurata and Xyrichtys novacula studied here, which showed highly diverse microbial community structures, dominated by Proteobacteria, mostly related to an aerobic or microaerophilic metabolism, but with some common shared major species, such as Ralstonia sp. On the other hand, farmed non-fasted S. aurata individuals had a microbial structure that mirrored the microbial composition of their food source, which was most likely anaerobic, since several members of the genus Lactobacillus, probably revived from the feed and enriched in the gut, dominated the communities. The most striking observation was that after a short fasting period (86 h), farmed gilthead seabream almost lost their whole gut microbiome, and the resident community associated with the mucosa had a very much reduced diversity that was highly dominated by a single potentially aerobic species Micrococcus sp., closely related to M. flavus. The results pointed to the fact that, at least for the juvenile S. aurata studied, most of the microbes in the gut were transient and highly dependent on the feed source, and that only after fasting for at least 2 days could the resident microbiome in the intestinal mucosa be determined. Since an important role of this transient microbiome in relation to fish metabolism could not be discarded, the methodological approach needs to be well designed in order not to bias the results. The results have important implications for fish gut studies that could explain the diversity and occasional contradictory results published in relation to the stability of marine fish gut microbiomes, and might provide important information for feed formulation in the aquaculture industry.This study was funded by the Spanish Ministry of Science and Innovation projects CTM2017-91490-EXP, PGC2018-096956-B-C41, RTC-2017-6405-1 and PID2021-126114NB-C42, which were also supported by the European Regional Development Fund (FEDER). RRM acknowledges financial support from a sabbatical stay at Helmholz Zentrum München by grant PRX21/00043, which was also from the Spanish Ministry of Science, Innovation and Universities. TV acknowledges the “Margarita Salas” postdoctoral grant, funded by the Spanish Ministry of Universities, within the framework of the Recovery, Transformation and Resilience Plan funded by the European Union (NextGenerationEU), with the participation of the University of the Balearic Islands (UIB). AP was supported by an FPI pre-doctoral fellowship (ref. FPI/2269/2019) from the Balearic Islands Government General Direction of Innovation and Research. AR was supported by a pre-doctoral grant (PRE2019-091259) linked to the ADIPOQUIZ project (RTI2018-095653-R-I00), funded by the Spanish Ministry of Science and Innovation.The research was carried out within the framework of the activities of the Spanish Government through the “Maria de Maeztu Centre of Excellence” accreditation to IMEDEA (CSIC-UIB) (CEX2021-001198).With funding from the Spanish government through the ‘María de Maeztu Unit of Excelence’ accreditation (CEX2021-001198).Peer reviewe

Automatic marine fish detection using deep learning under laboratory conditions.

[eng] In the last decade, deep learning has revolutionized almost every scientific discipline and everyday tasks. In behavioural ecology, deep learning allows us to automatize the acquisition of animal behaviour and improve the analysis of large amounts of behavioural data. Here, we have trained an image-based deep learning algorithm, the Faster R-CNN (Faster region-based convolutional neural network), to automatically detect a marine fish under laboratory conditions, aiming to obtain an automatic tool to study fish behaviour from video recordings. For the training, we have used a total of 14000 labelled images and a data augmentation technique to explore the performance of the fish detection algorithm. Then, we have validated its functioning at different training and augmentation degrees, processing more than 52039 frames for every validation, with and without the presence of the marine fish, Sparus aurata in normal and altered (introduction of a novel object) laboratory conditions. The neural network in its final and best version, trained with all the images and with data augmentation, reached an accuracy of 93%, proving to be a good instrument to study fish behavioural ecology in a non-invasive way

Novel computer vision tools applied to marine recreational fisheries spatial planning

© 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)Successful marine spatial planning relies on understanding patterns of human use, with accurate, detailed, and up-to-date information about the spatial distribution of fishing effort. In commercial vessels, tracking systems like the vessel monitoring system (VMS) or the automatic identification system (AIS) have helped to maintain and enhance the biodiversity of areas by generating large sources of positional data that served for commercial marine spatial planning. However, there is no regulation regarding location systems such as VMS or AIS for marine recreational fishing boats. Obtaining spatial data on marine recreational fishing can be difficult and time-intensive given the widespread and variable nature of the fleet. Remote cameras and computer vision systems are increasingly used to overcome the cost limitations of these conventional methods. Here we show a novel high-resolution and low-cost tracking system based on photo time-lapses and state-of-the-art computer vision algorithms, including deep learning, to automatically classify and obtain precise trajectories of fishing and cruising boats in coastal areas. Our method contributes to the automatic surveillance of marine protected areas by providing an image-based tool for automatic, real-time monitoring. Our method also allows for determining the intensity and spatial-temporal distribution of recreational fishing effort, important to defining the sustainability of the activity and coastal areas. We finally discuss the opportunities and limitations of computer vision tools applied to marine recreational fisheries spatial planning.The present research was carried out within the framework of the activities of the Spanish Government through the "Maria de Maeztu Centre of Excellence" accreditation to IMEDEA (CSIC-UIB) (CEX2021–001198). This work received funding from the METARAOR project (grant no. PID2022–139349OB-I00), JSATS PIE project (grant no. PIE202030E002) funded by MCIN/AEI/10.13039/501100011033 and AutoNatura 2000 Tres founded by the Fundación Biodiversidad (PLEAMAR program).With funding from the Spanish government through the ‘María de Maeztu Unit of Excelence’ accreditation (CEX2021-001198-M).Peer reviewe

The isotopic niche of Atlantic, biting marine mammals and its relationship to skull morphology and body size

Understanding the trophic niches of marine apex predators is necessary to understand interactions between species and to achieve sustainable, ecosystem-based fisheries management. Here, we review the stable carbon and nitrogen isotope ratios for biting marine mammals inhabiting the Atlantic Ocean to test the hypothesis that the relative position of each species within the isospace is rather invariant and that common and predictable patterns of resource partitioning exists because of constrains imposed by body size and skull morphology. Furthermore, we analyze in detail two species-rich communities to test the hypotheses that marine mammals are gape limited and that trophic position increases with gape size. The isotopic niches of species were highly consistent across regions and the topology of the community within the isospace was well conserved across the Atlantic Ocean. Furthermore, pinnipeds exhibited a much lower diversity of isotopic niches than odontocetes. Results also revealed body size as a poor predictor of the isotopic niche, a modest role of skull morphology in determining it, no evidence of gape limitation and little overlap in the isotopic niche of sympatric species. The overall evidence suggests limited trophic flexibility for most species and low ecological redundancy, which should be considered for ecosystem-based fisheries management

Chronotypes-personality behavioural syndromes in wild marine fish

Chronotypes, the individual differences in daily activity timing, have profound associations with numerous physiological processes. Despite this, the covariance between chronotypes and other aspects of an individual's behaviour has been infrequently explored in non-human animals. This study delves into individual's variation across four axes of personality in a controlled environment, utilising the pearly razorfish, a model species for fish chronotype studies. We identified behavioural types across the aggressiveness continuum and established behavioural syndromes amongst exploration, activity, and boldness, irrespective of body size and condition. Subsequent to this, the experimental subjects were reintroduced to their natural habitat and individually tracked using high-resolution technology to ascertain their chronotypes. Our results revealed that whilst the exploration-activity-boldness syndrome bore no correlation with chronotypes, a significant association was observed between aggressiveness and chronotype. Hence, individuals with later awakening times and rest onsets were more aggressive than their counterparts with earlier awakening times and rest onsets. This study provides pioneering evidence linking fish chronotypes with other behavioural traits, such as aggressiveness, suggesting that behavioural variation could be potentially linked to the individuals' variation in internal clocks and the environmental variables influencing their expression.This work received funding from the CLOCKS I+D+i project (grant no. PID2019-104940GA-I00) funded by MCIN/AEI/10.13039/501100011033. This manuscript is a contribution of the Joint Research Unit IMEDEA-LIMIA. The present research was carried out within the framework of the activities of the Spanish Government through the "Maria de Maeztu Centre of Excellence" accreditation to IMEDEA (CSIC-UIB) (CEX2021-001198). The telemetry system for free-living tracking was financed by the German Federal Ministry of Education and Research (Grant No. #033W024A). Martina Martorell-Barceló was supported by an FPI predoctoral fellowship from the Direcció General de Innovació I Recerca of the Balearic Islands Government (ref. FPI/2167/2018). Eneko Aspillaga was supported by Margalida Comas (ref. PD/023/2018) and Vicenç Mut (PD/041/2021) Postdoctoral Grants from the Government of the Balearic Islands and the European Social Fund. Margarida Barcelo-Serra received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. WildFishGenes-891404.With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2021-001198).Peer reviewe

Aggressiveness-related behavioural types in the pearly razorfish [dataset]

Los datos fueron generados manualmente a través de la visualización de videos de los experimentos. Fueron introducidos en RStudio Team (2020), donde se analizaron para la obtención de los resultados.-- este conjunto de datos es original de este trabajo. No se ha usado datos de estudios preliminares.-- Datos recogidos en experimentos realizados en el Laboratorio de Investigaciones Marinas y Acuicultura (LIMIA) en Mallorca. Los individuos experimentales fueron capturados en la Bahía de Palma, Mallorca.This data set is supplementary material for the article "Types of behaviour related to aggressiveness in pearlescent fish". Animal personality has a very relevant implication in a multitude of eco-evolutionary processes. It is a topic very approached in freshwater fish, not so in marine species, because its captivity is a challenge to reproduce its natural habitat. this is the first evidence of behavioural traits in the pearly razorfish. For this, we designed experiments in the laboratory, where the experimental individuals were subjected to the mirror test—a widely used test to determine each individual's aggressiveness. By not recognizing their reflection in the mirror, fish perceive their reflection as the intrusion of another individual into their territory. Thanks to these experiments, we were able to determine each individual's aggressiveness score, finding significant differences between individuals. Differences found regardless of height, sex or individual condition. These findings suggest that this species' aggressiveness may have a genetic origin, as has been demonstrated in other species.Este trabajo ha recibido financiación del Proyecto CLOCKS I + D + i (subvención no. PID2019-104940GA-I00) financiado por el MICINN y la Agencia Estatal de Investigación, y del proyecto de investigación intramuros JSATS (subvención no. PIE202030E002) financiado por la MICINN y Consejo Nacional de Investigaciones Científicas (CSIC). Martina Martorell-Barceló contó con una beca pre doctoral FPI (ref. FPI / 2167/2018) de la Dirección General de Innovación e Investigación del Gobierno de las Illes Balears. Josep Alós ha recibido una Beca Ramón y Cajal (beca nº. RYC2018-024488-I) financiada por el Ministerio de Ciencia e Innovación (MICINN). Margarida Barcelo-Serra fue apoyada por una MSCA-IF (subvención núm. WildFishGenes-891404).N

Aggressiveness-related behavioural types in the pearly razorfish

Behavioural types (i.e., personalities or temperament) are defined as among individual differences in behavioural traits that are consistent over time and ecological contexts. Behavioural types are widespread in nature and play a relevant role in many ecological and evolutionary processes. In this work, we studied for the first time the consistency of individual aggressiveness in the pearly razorfish, Xyrichtys novacula, using a mirror test: a classic method to define aggressive behavioural types. The experiments were carried out in semi-natural behavioural arenas and monitored through a novel Raspberry Pi-based recording system. The experimental set up allowed us to obtain repeated measures of individual aggressivity scores during four consecutive days. The decomposition of the phenotypic variance revealed a significant repeatability score (R) of 0.57 [0.44–0.60], suggesting high predictability of individual behavioural variation and the existence of different behavioural types. Aggressive behavioural types emerged irrespective of body size, sex and the internal condition of the individual. Razorfishes are a ubiquitous group of fish species that occupy sedimentary habitats in most shallow waters of temperate and tropical seas. These species are known for forming strong social structures and playing a relevant role in ecosystem functioning. Therefore, our work provides novel insight into an individual behavioural component that may play a role in poorly known ecological and evolutionary processes occurring in this species.This work was carried out as part of the research project Cronofish (AAEE 101/2017) funded by Balearic Islands Government. In addition, this project also received financing from the CLOCKS project from the Spanish Government (PID2019-104940GA-I00). Martina Martorell-Barceló was supported by an FPI predoctoral fellowship (ref. FPI/2167/2018) from the Balearic Islands Government General Direction of Innovation and Research. Josep Alós was supported by a Ramon y Cajal Grant (grant no. RYC2018-024488-I) and the intramural research project JSATS (grant no. PIE 202030E002) funded by the Spanish Ministry of Science and Innovation, and the Spanish National Research Council