1. INTRODUCTION <em>MalaMix </em>is a compiled metabarcoding dataset composed of 451 marine samples collected from a range of depths - from the surface (3m) to deep waters (as far down as 4800m). This dataset covers three ocean layers: the epi- (0-200m – including DCM), meso- (200-1000m) and bathypelagic (1000-4000m). <em>MalaMix</em> combines samples obtained during two oceanographic expeditions with similar sampling strategies: i) the Malaspina-2010 global expedition that produced 263 samples collected between December 2010 and July 2011 from 120 stations distributed along the tropical and subtropical portions (latitudes between 35° N and 40° S) of the Pacific, Atlantic and Indian oceans; and ii) the <em>HotMix</em> trans-Mediterranean cruise that produced 188 samples collected between April and May 2014 in 29 stations distributed along the whole Mediterranean Sea (from -5° W to 33° E) and the adjacent Northeast Atlantic Ocean. <em>MalaMix</em> comprises: a 16S-V4V5 rRNA gene ASV table (MalaMix_16S.csv); an 18S-V4 rRNA gene ASV table (MalaMix_18S.csv); two tables of contextual metadata (MalaMix_EnvData_16S and MalaMix_EnvData_18S) including 6 standardized environmental parameters (temperature [°C], salinity, fluorescence, PO<sub>4</sub><sup>3− </sup>[µmol L<sup>-1</sup>], NO<sub>3</sub><sup>− </sup>[µmol L<sup>-1</sup>], and SiO<sub>2 </sub>[µmol L<sup>-1</sup>]) as well as species taxonomic and phylogenetic diversity metrics a table (MalaMix_FCdata.csv) with flow cytometry microbial counts [cell mL<sup>-1</sup>] and bacterial activity measurements [pmol Leu L<sup>-1</sup> h<sup>-1</sup>]; a README file (README_Metadata.csv) describing the meaning and units of each variable column in the metadata tables. The raw DNA sequences are publicly available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena) under accession numbers PRJEB23913 [18S rRNA genes] & PRJEB25224 [16S rRNA genes] for the Malaspina surface dataset; PRJEB23771 [18S rRNA genes] & PRJEB45015 [16S rRNA genes] for the Malaspina vertical profiles; PRJEB45011 [16S rRNA genes] & PRJEB45014 [18S rRNA genes] for the Malaspina deep sea dataset; and PRJEB44683 [18S rRNA genes] & PRJEB44474 [16S rRNA genes] for the HotMix expedition. Further methodological details are available here: https://www.biorxiv.org/content/10.1101/2023.01.13.523743v1 2. FUTURE FORMAT CHANGES No major changes are expected for the main general format of the database. 3. ACKNOWLEDGMENTS The current dataset was generated with funds from the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain), MicroEcoSystems (240904, RCN, Norway), MINIME (PID2019-105775RB-I00, AEI, Spain), and PID2021-125469NB-C31 (AEI, Spain), as well as DOREMI (CTM2012-34294) and HOTMIX (CTM2011-30010-C02-01 and CTM2011-30010-C02-02) of the Spanish Ministry of Economy and Innovation, co-financed with FEDER funds. 4. COPYRIGHT NOTICE<br> <br> This database is provided “as is” and without any warranty of any kind, of openly available for non-commerical purposes (CC BY-NC). <strong>CC BY-NC</strong> means that users can make use of the work (including copying, distributing, adapting and building upon the work), but only for noncommercial purposes and as long as attribution is given to the creator: https://oabooks-toolkit.org/lifecycle/article/4012101-choosing-a-license
Accurately forecasting the response of global biota to warming is a fundamental challenge for ecology in the Anthropocene. Within-species variation in thermal sensitivity, caused by phenotypic plasticity and local adaptation of thermal limits, is often overlooked in assessments of species responses to warming. Despite this, implicit assumptions of thermal niche conservatism or adaptation and plasticity at the species level permeate the literature with potentially important implications for predictions of warming impacts at the population level. Here we review how these attributes interact with the spatial and temporal context of ocean warming to influence the vulnerability of marine organisms. We identify a broad spectrum of thermal sensitivities among marine organisms, particularly in central and cool-edge populations of species distributions. These are characterized by generally low sensitivity in organisms with conserved thermal niches, to high sensitivity for organisms with locally adapted thermal niches. Important differences in thermal sensitivity among marine taxa suggest that warming could adversely affect benthic primary producers sooner than less vulnerable higher trophic groups. Embracing the spatial, temporal and biological context of within-species variation in thermal physiology helps explain observed impacts of ocean warming and can improve forecasts of climate change vulnerability in marine systems. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.
Gff and fasta files of dust-associated MAGs that were analyzed on GRiD for estimation of in situ replication rates
Detrital carbon accumulation accounts for most of an ecosystem's capacity to store organic carbon because the carbon contained as plant detritus exceeds that stored in living plants by about threefold. A comparative analysis of the mass and turnover of detrital carbon in ecosystems demonstrates that these properties are strongly related to the turnover rate of the dominant primary producers and are poorly related to ecosystem primary production. These results contribute to an understanding of the factors that control carbon storage in ecosystems and the role of carbon storage in the global carbon budget.
AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 36:41-52 (2004) - doi:10.3354/ame036041 Response of bacterial grazing rates to experimental manipulation of an Antarctic coastal nanoflagellate community Dolors Vaqué1,*, Susana Agustí2, Carlos M. Duarte2 1Institut de Ciències del Mar de Barcelona-CMIMA, CSIC, Departament de Biologia Marina i Oceanografia, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalunya, Spain 2IMEDEA (CSIC-UIB), Institut Mediterrani d¹Estudis Avançats, Miquel Marquès, 21, 07190 Esporles, Mallorca, Illes Balears, Spain *Email: dolors@icm.csic.es ABSTRACT: We examined changes of bacterial losses related to heterotrophic nanoflagellate (HNF) size distribution in late spring/early summer (1998/1999) using 9 grazing experiments in a coastal Antarctic area (Johnson¹s Dock, Livingston Island, Bransfield Sector). Water samples were subjected to size fractionation through 50 and 5 μm pore sizes to obtain a truncation of the microbial food web. In each fraction, we estimated bacterial loss rates and abundance and biomass of HNF grouped into 4 size classes (≤2, 2 to 5, 5 to 10, 10 to 20 μm). We also investigated whether grazing on bacteria was mainly due to HNF, and which HNF size class had a major impact on bacteria. We expected that in the 50 μm fraction, large protists (ciliates, dinoflagellates) would prey preferentially on nanoprotists and relieve bacterial pressure from HNF. Bacterial grazing rates were estimated by disappearance of fluorescently labeled bacteria over 24 h. These showed similar values in both experimental treatments, although they were slightly higher for the 50 μm fraction. Average grazing rates were 4.8 × 105 ± 3.6 ×: 105 cells ml-1 d-1 in the 5 μm treatment and 6.9 ×: 105 ± 3.2 ×: 105 cells ml-1 d-1 for the 50 μm fraction. In the 5 μm fraction, HNF abundance (integrated over 24 h, HNFi) and bacterial grazing rates were significantly related. The best relationship was obtained with the smallest HNFi size classes (from ≤2 and 2 to 5 μm). In the 50 μm fraction, no relationships were found between bacterial loss rate and both total HNFi and any HNFi size class in terms of abundance and biomass. However, microozooplankton was negatively related to total bacteria and both HNFi abundance and biomass. The major contributor to this negative relationship was the HNFi size classes from ≤2 and 2 to 5 μm. Consequently, and against our expectations, large protists contributed to microbial food-web complexity by masking carbon fluxes from bacteria to HNF, and by feeding on both bacteria and nanoprotists. KEY WORDS: Antarctica · Johnson¹s Dock · Bacteria · Heterotrophic nanoflagellate size · Phagotrophic · Ciliates · Dinoflagellates · Grazing Full article in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 36, No. 1. Online publication date: June 24, 2004 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2004 Inter-Research.
In oligotrophic ecosystems, bacterial production (BP) via the microbial loop and grazing processes plays a crucial role in carbon transfer (CT) to higher trophic levels. However, there studies quantifying CT from bacteria to the marine food web are limited. In this study, we used 13 C-isotope tracers and cavity ring-down spectroscopy to measure primary production (PP), BP, bacterial respiration (BR), and CT within the microbial food web in oligotrophic waters. Our results revealed that the BP rate, ranging from 0.02 to 4.93 μg C L −1 d −1 , was significantly lower than the total PP, which ranged from 2.69 to 16.71 μg C L −1 d −1 . Our findings indicate that grazing of bacteria in the Red Sea is substantial. The removal of grazers through prefiltration lead to a 9.5-fold increase in BP rates, rising from 0.37 ± 0.04 μg C L −1 d −1 to 3.52 ± 1.04 μg C L −1 d −1 at the stations analyzed. This significant increase suggests that a large portion of bacterial carbon is rapidly transfer to higher trophic levels via grazing. In addition, carbon transfer (CT) to the food web, measured in size fractions above picoplankton (&gt;1.2 or &gt; 3 μm), accounted for an average of 72.7 ± 4.0% of the net bacterial production (Net BP = BP + CT), underscore the crucial role of grazers in bacterial carbon cycling. This transfer increased significantly with increasing temperatures, highlighting the enhanced role of the microbial loop in CT during warmer conditions. We found that at some stations, a large proportion of the carbon assimilated by bacteria was used for respiration, averaging 1.37 ± 0.54 μg C L −1 d −1 . This high respiratory demand of bacterial cells in oligotrophic waters may explain the low bacterial growth efficiency (BGE) of 9.7% ± 1.0% observed in our study, along with the significant correlation between BP and BGE. Our findings demonstrated that BP effectively transfers carbon through the microbial loop to higher trophic levels in the oligotrophic and warm waters of the Red Sea.
(1994). Environmental factors controlling the life history of Procambarus clarkii (Decapoda, Cambaridae) in a temporary marsh of the Doñana National Park (SW Spain) SIL Proceedings, 1922-2010: Vol. 25, No. 4, pp. 2450-2453.
Biologging is a scientific endeavor that studies the environment and animals within it by outfitting the latter with sensors of their dynamics as they roam freely in their natural habitats. As wearable technologies advance for the monitoring of human health, it may be instructive to reflect on the successes and failures of biologging in field biology over the past few decades. Several lessons may be of value. Physiological sensors can "encode" for a wider number of states than the one explicitly targeted, although the limits of this are debatable. The combination of orthogonal sensors turns out to be critical to delivering a high value data set. Sensor fusion and engineering for longevity are also important for success. This Perspective highlights successful strategies for biologging that hold promise for human health monitoring.
Global Change has been defined as the impact of human activities on the key processes that determine the functioning of the Biosphere. Global Change is a major threat for marine ecosystems and includes climate change as well as other global impacts such as inputs of pollutants, overfishing and coastal sprawl. The Semi-enclosed Arabian Seas, including the Arabian Gulf and the Red Sea, have supported human livelihoods in the Arabian Peninsula over centuries and continue to do so, but are also threatened by Global Change. These threats are particularly severe as Semi-enclosed Arabian Seas already present rather extreme conditions, in terms of temperature, salinity and oxygen concentration. The vulnerability of the unique marine ecosystems of the Semi-enclosed Arabian Seas to Global Change vectors is largely unknown, but predictions based on first principles suggest that they may be at or near the tipping point for many pressures, such as warming and hypoxia. There is an urgent need to implement international collaborative research programs to accelerate our understanding of the vulnerability of Semi-enclosed Arabian Seas to Global Change vectors in order to inform conservation and management plans to ensure these Seas continue to support the livelihoods and well-being of the Arab nations.
Poster: ECR 2016 / C-2165 / Optimisation of DBT using parallel computing aiming to reduce patient dose by: P. R. T. Ferreira 1, C. Duarte1, N. Oliveira1, L. Janeiro1, A. Silva1, M. L. Orvalho1, P. Medeiros2, N. Matela1; 1Lisbon/PT, 2Caparica/PT