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Section: Genomics ; Topics: Biology of interactions, Ecology, Genetics/genomics

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

Barnabé, Christian; Sempéré, Guilhem; Manzanilla, Vincent; Millan, Joel Moo; Amblard-Rambert, Antoine; Waleckx, Etienne

10.24072/pcjournal.501 - Peer Community Journal, Volume 4 (2024), article no. e114.
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We developed a python package called mbctools, designed to offer a cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle the most common tasks in metabarcoding pipelines such as paired-end merging, primer trimming, quality filtering, sequence denoising, zero-radius operational taxonomic unit (ZOTU) filtering, and has the capability to process multiple genetic markers simultaneously. mbctools is a menu-driven program that eliminates the need for expertise in command-line skills and ensures documentation of each analysis for reproducibility purposes. The software, designed to run in a console, offers an interactive experience, guided by keyboard inputs, assisting users along the way through data processing and hiding the complexity of command lines by letting them concentrate on selecting parameters to apply in each step of the process. In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon-based Next-Generation Sequencing data. This software is a versatile open-source tool for processing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. It provides functions for various tasks such as dereplication, clustering, chimera detection, and taxonomic assignment. VSEARCH is thus very efficient in retrieving the overall diversity of a sample. To adapt to the diversity of projects in metabarcoding, we facilitate the reprocessing of datasets with the possibility to adjust parameters. mbctools can also be launched in a headless mode, making it suited for integration into pipelines running on High-Performance Computing environments. mbctools is available at https://github.com/GuilhemSempere/mbctools, https://pypi.org/project/mbctools/.
Section: Microbiology ; Topics: Microbiology

The effect of dietary fish oil replacement by microalgae on the gilthead sea bream midgut bacterial microbiota

Katsoulis-Dimitriou, Stefanos; Nikouli, Eleni; Gkalogianni, Elli Zafeiria; Karapanagiotidis, Ioannis T.; Kormas, Konstantinos A.

10.24072/pcjournal.498 - Peer Community Journal, Volume 4 (2024), article no. e113.
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It is well known that the gut microbiome and its interaction with the host influence several important factors for fish health such as nutrition and metabolism. Diet is one of the main factors influencing the composition of the gut microbiome in reared fish. Microalgae, due to their high fatty acid content, appear to be a promising alternative for replacing fish oil in aquafeed. Thus, the aim of this work was to evaluate the effects of dietary microalgae blends as fish oil replacers οn the midgut bacterial microbiota of the gilthead sea bream (Sparus aurata). The control diet (FO) contained only fish oil as a source of lipids, EPA and DHA fatty acids, while three experimental diets were used where fish oil was replaced at 67% by one of the following microalgae biomass blends: Microchloropsis gaditana and Isochrysis sp. (Tisochrysis lutea) (MI), Phaeodactylum tricornutum and Isochrysis sp. (PI) and Schizochytrium sp. and P. tricornutum (SP). The midgut bacterial community composition of the experimental diets was altered compared to the control diet. There were 11 operational taxonomic units (OTUs) that were highly abundant in FO compared to the three experimental diets (FO, MI, SP) and two OTUs that were found in high abundance in both FO and the experimental diets in all comparisons (FO-MI, FO-PI, FO-SP). Most of the highly abundant OTUs in the experimental diets were unique to each experimental diet, with two OTUs being found in common between FO-MI and FO-PI. Additional evidence from the presumptive bacterial functional metabolic pathways suggested that the microalgae-based diets resulted in one over-expressed and one under-expressed pathway. The overexpressed pathway was related to the metabolism of fucose, a major constituent of the polysaccharide content of several microalgal species. Peptidoglycan biosynthesis was the under-expressed metabolic pathway. This suggests that a new gut microbiota profile was selected due to the microalgae inclusion in the provided diet. This study showed that, with the absence of mortality in fish, the gilthead sea bream gut microbiome can smoothly adapt its function according to the metabolic capacity of the dietary microalgae combinations that were used. The MI feed seems to promote several beneficial bacteria with potential probiotic abilities in the fish gut, belonging to the Pseudoalteromonas, Pseudomonas, Bacillus and Rhodopseudomonas genera.
Section: Ecology ; Topics: Ecology, Environmental sciences

Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons

Jones, Auriane G.; Schaal, Gauthier; Boyé, Aurélien; Creemers, Marie; Derolez, Valérie; Desroy, Nicolas; Fiandrino, Annie; Mouton, Théophile L.; Simier, Monique; Smith, Niamh; Ouisse, Vincent

10.24072/pcjournal.499 - Peer Community Journal, Volume 4 (2024), article no. e112.
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Coastal lagoons are transitional ecosystems that host a unique diversity of species and support many ecosystem services. Owing to their position at the interface between land and sea, they are also subject to increasing human impacts, which alter their ecological functioning. Because coastal lagoons are naturally highly variable in their environmental conditions, disentangling the effects of anthropogenic disturbances like eutrophication from those of natural variability is a challenging, yet necessary issue to address. Here, we analyze a dataset composed of macrobenthic invertebrate abundances and environmental variables (hydro-morphology, water, sediment and macrophytes) gathered across 29 Mediterranean coastal lagoons located in France, to characterize the main drivers of community composition and structure. Using correlograms, linear models and variance partitioning, we found that lagoon hydro-morphology (connection to the sea and lagoon surface), which affects the level of environmental variability (salinity and temperature), as well as lagoon-scale benthic habitat diversity (using macrophyte morphotypes) seemed to regulate macrofauna distribution, while eutrophication and associated stressors like low dissolved oxygen, acted upon the existing communities, mainly by reducing species richness and diversity. Furthermore, M-AMBI, a multivariate index composed of species richness, Shannon diversity and AMBI (AZTI's Marine Biotic Index) and currently used to evaluate the ecological state of French coastal lagoons, was more sensitive to eutrophication (18%) than to natural variability (9%), with nonetheless 49% of its variability explained jointly by both. To improve the robustness of benthic indicators like M-AMBI and increase the effectiveness of lagoon benthic habitat management, we call for a revision of the ecological groups at the base of the AMBI index and of the current lagoon typology which could be inspired by the lagoon-sea connection levels used in this study.
Section: Ecology ; Topics: Ecology, Population biology, Statistics ; Conference: Euring 2023

Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird

Nater, Chloé R.; Frassinelli, Francesco; Martin, James A.; Nilsen, Erlend B.

10.24072/pcjournal.494 - Peer Community Journal, Volume 4 (2024), article no. e111.
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Quantifying temporal and spatial variation in animal population size and demography is a central theme in ecological research and important for directing management and policy. However, this requires field sampling at large spatial extents and over long periods of time, which is not only prohibitively costly but often politically untenable. Participatory monitoring programs (also called citizen science programmes) can alleviate these constraints by recruiting stakeholders and the public to increase the spatial and temporal resolution of sampling effort and hence resulting data. While the majority of participatory monitoring programs are limited by opportunistic sampling designs, we are starting to see the emergence of structured citizen science programs that employ trained volunteers to collect data according to standardized protocols. Simultaneously, there is much ongoing development of statistical models that are increasingly more powerful and able to make more efficient use of field data. Integrated population models (IPMs), for example, are able to use multiple streams of data from different field monitoring programmes and/or multiple aspects of single datasets to estimate population sizes and key vital rates. Here, we developed a multi-area version of a recently developed integrated distance sampling model (IDSM) and applied it to data from a large-scale participatory monitoring program – the “Hønsefuglportalen” – to study spatio-temporal variation in population dynamics of willow ptarmigan (Lagopus lagopus) in Norway. We constructed an open and reproducible workflow for exploring temporal, spatial (latitudinal, longitudinal, altitudinal), and residual variation in recruitment, survival, and population density, as well as relationships between vital rates and relevant covariates and signals of density dependence. Recruitment rates varied more across space than over time, while the opposite was the case for survival. Slower life history patterns (higher survival, lower recruitment) appeared to be more common at higher latitudes and altitudes, portending differential effects of climate change on ptarmigan across their range. While there was variation in the magnitude of the effect small rodent occupancy had on recruitment, the relationships were predominantly positive and thus consistent with the alternative prey hypothesis. Notably, the accurate estimation of covariate effect was only made possible by integrating data from several monitoring areas for analysis. Our study highlights the potential of participatory monitoring and 2integrated modelling approaches for estimating and understanding spatio-temporal patterns in species abundance and demographic rates, and showcases how corresponding workflows can be set up in reproducible and semi-automated ways that increase their usefulness for informing management and regular reporting towards national and international biodiversity frameworks.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA