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Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef's approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial diversity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef's Mandala with the aim of improving future studies on aquatic microbial ecology.

[EN] Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef’s approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial diversity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef’s Mandala with the aim of improving future studies on aquatic microbial ecology., [ES] Ramon Margalef fue un científico pionero que introdujo un enfoque interdisciplinario a los estudios ecológicos. Sus estudios fueron de los primeros en incorporar diferentes conceptos en la literatura de la ecología acuática, desde los organismos y las interacciones de los ecosistemas hasta la evolución. Para llevar el enfoque de Margalef a los estudios científicos actuales, en este articulo exploramos su visión de la ecología acuática dentro de cuatro campos de estudio interrelacionados: teoría ecológica, diversidad microbiana, ciclos biogeoquímicos y cambios ambientales globales. Inspirándonos en sus estudios pasados, analizamos en este texto los desafíos científicos actuales y proponemos un enfoque integrado considerando el concepto unificador del Mandala de Margalef con el objetivo de mejorar los estudios futuros sobre la ecología microbiana acuática

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Howell, K. L., Hilario, A., Allcock, A. L., Bailey, D. M., Baker, M., Clark, M. R., Colaco, A., Copley, J., Cordes, E. E., Danovaro, R., Dissanayake, A., Escobar, E., Esquete, P., Gallagher, A. J., Gates, A. R., Gaudron, S. M., German, C. R., Gjerde, K. M., Higgs, N. D., Le Bris, N., Levin, L. A., Manea, E., McClain, C., Menot, L., Mestre, N. C., Metaxas, A., Milligan, R. J., Muthumbi, A. W. N., Narayanaswamy, B. E., Ramalho, S. P., Ramirez-Llodra, E., Robson, L. M., Rogers, A. D., Sellanes, J., Sigwart, J. D., Sink, K., Snelgrove, P. V. R., Stefanoudis, P., V., Sumida, P. Y., Taylor, M. L., Thurber, A. R., Vieira, R. P., Watanabe, H. K., Woodall, L. C., & Xavier, J. R. A blueprint for an inclusive, global deep-sea ocean decade field program. Frontiers in Marine Science, 7, (2020): 584861, doi:10.3389/fmars.2020.584861., The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper (> 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea res, Development of this paper was supported by funding from the Scientific Committee on Oceanic Research (SCOR) awarded to KH and AH as working group 159 co-chairs. KH, BN, and KS are supported by the UKRI funded One Ocean Hub NE/S008950/1. AH work is supported by the CESAM (UIDP/50017/2020 + 1432 UIDB/50017/2020) that is funded by Fundação para a Ciência e a Tecnologia (FCT)/MCTES through national funds. AA is supported by Science Foundation Ireland and the Marine Institute under the Investigators Program Grant Number SFI/15/IA/3100 co-funded under the European Regional Development Fund 2014–2020. AC is supported through the FunAzores -ACORES 01-0145-FEDER-000123 grant and by FCT through strategic project UID/05634/2020 and FCT and Direção-Geral de Politica do Mar (DGPM) through the project Mining2/2017/005. PE is funded by national funds (OE), through FCT in the scope of the framework contract foreseen in the numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19. SG research is supported by CNRS funds. CG is supported by an Independent Study Award and the Investment in Science Fund at WHOI. KG gratefully acknowledges support from Synchronicity Earth. LL is funded by the NOAA Office of Ocean Exploration and Research (NA19OAR0110305) and the US National Science Foundation (OCE 1634172). NM is supported by FCT and DGPM, through the project Mining2/2017/001 and the FCT grants CEECIND/00526/2017, UIDB/00350/2020 + UIDP/00350/2020. SR is funded by the FCTgrant CEECIND/00758/2017. JS is supported by ANID FONDECYT #1181153 and ANID Millennium Science Initiative Program #NC120030. JX research is funded by the European Union’s Horizon 2020 research and innovation program through the SponGES project (grant agreement no. 679849) and further supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020. The Natural Sciences and Engineering Council of Canada supports AM and PVRS. MB and th

The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper (> 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea res

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep‐sea physico‐chemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4000 m) free‐living and particle‐attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physico‐chemical conditions. Amino acid‐like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200‐1000 m) communities, suggesting a direct connectivity through fast‐sinking particles that escapes mesopelagic transformations. Finally, we identified a pool of endemic deep‐sea prokaryotic taxa (including potential chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physico‐chemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters

Background: The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans. Results: We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal-like”- abundant and ubiquitous; “logistic”- globally rare, present in few sites; and “bimodal”- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal-like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal-like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members

La mayor parte de la vida en el mar se encuentra en los primeros 200 metros, mientras que el océano profundo -hasta los 4.000 metros- está casi 'despoblado'. A pesar de estas diferencias, un grupo de científicos ha constatado que la biodiversidad microbiana de ambas zonas está íntimamente conectada

The smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts that selection, dispersal and drift are main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change

The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean communities

[EN] Microorganisms in the ocean conform an extensive microbiome where individuals interact constantly with the particulate matter. However, most of the studies have focused on the free-living microorganisms, and to a lesser extent on the attached microorganisms but have not taken into account the organisms associated to particles of different sizes. The main objective of this thesis is to characterize the diversity of prokaryotes along the particulate matter continuum present in the ocean, as well as to describe its temporal and spatial variability at distinct scales. First of all, we propose a multiple size-fractionation as a sampling method that provides a better comprehension of the prokaryotic diversity than the commonly used sampling methods. Our work shows that each size-fraction contains distinct prokaryotic communities that vary at different spatial and temporal scales. In general, there is an increase of bacterial richness from the smaller to the larger particles, suggesting that larger particles may contribute with new niches. The main exception is the bathypelagic, where richness decreases form the small to the largest size-fractions. In contrast, Archaea presented higher richness in the smaller size-fractions and, although had lower diversity and relative abundance than bacteria, these increased with depth. We moreover classified taxonomic groups depending on whether they have preference for small size-fractions, for larger size-fractions, or do not have a clear preference for any size fraction. This classification is presented as an alternative to the traditional simple separation between free-living bacteria and attached bacteria. Most of the taxonomic groups maintain their preference for certain size fractions in space and time, although some taxonomic groups change their preferences in vertical profiles from the surface to the bathypelagic and along time. We also observed that the bathypelagic is dominated by prokaryotes which are also present in su, [CAT] Els microoganismes oceànics conformen un extens microbioma on els individus interactuen constantment amb la matèria particulada. No obstant això, la gran majoria dels estudis d’ecologia dels microorganismes no tenen en compte aquells associats a la matèria particulada o, si els tenen en compte, no consideren les diferents grandàries que presenten les partícules. L’objectiu principal de la present tesi és la caracterització de la diversitat de procariotes al llarg del continu de mides de les partícules marines presents a l’oceà, així com també descriure la seva variabilitat temporal i espacial a diferents escales. Primer de tot, proposem un fraccionament múltiple de mides de partícules com a mètode de mostreig que proporciona una millor comprensió de la diversitat procariòtica que els mètodes de mostreig més habituals. El nostre treball indica que cada fracció de mida presenta comunitats procariòtiques diferents que a més varien en l’espai, en el temps, i a diferents escales. En general, hi ha un increment de la riquesa de les comunitats bacterianes des de les partícules petites a les més grans, la qual cosa suggereix que les partícules més grans contribueixen nous nínxols ecològics. L’excepció a aquesta tendència s’observa en el batipelàgic, on la riquesa disminueix des de la fracció petita cap a les grans. Per contra, els arqueus presenten en general més riquesa en les fraccions més petites. Comparant bacteris i arqueus, aquests últims presenten menor diversitat i abundàncies relatives, però la seva rellevància augmenta des de la superfície de l’oceà cap al batipelàgic. Hem classificat els grups taxonòmics bacterians segons si tenen preferència per fraccions petites, preferència per fraccions grans, o si no presenten una preferència clara per fraccions petites o grans. Aquesta classificació es presenta com una alternativa a la tradicional separació simple entre bacteris de vida lliure o associats a partícules. La major part de grups taxonòmics mantenen en l’e, [ES] Los microoganismos oceánicos conforman un extenso microbioma donde los individuos interactúan constantemente con la materia particulada. Sin embargo, la gran mayoría de los estudios de microorganismos no tienen en cuenta aquellos asociados a la materia particulada o, si los tienen en cuenta, no consideran los distintos tamaños que presentan las partículas. El objetivo principal de la presente tesis es la caracterización de la diversidad de procariotas a lo largo del continuo de tamaños de las partículas marinas presentes en el océano, así como también describir su variabilidad temporal y espacial a distintas escalas. Primero de todo, proponemos un fraccionamiento múltiple de tamaños de partículas como método de muestreo que proporciona una mejor comprensión de la diversidad procariótica que los métodos de muestreo comunes. Nuestro trabajo indica que cada fracción de tamaño presenta comunidades procarióticas distintas que además varían en el espacio, en el tiempo, y a distintas escalas. En general, existe un incremento de la riqueza de las comunidades bacterianas desde las partículas pequeñas a las más grandes, sugiriendo que las partículas más grandes contribuyen nuevos nichos ecológicos. La excepción a esta tendencia se observa en el batipelágico, donde la riqueza disminuye desde la fracción pequeña hacia las grandes. Por el contrario, las arqueas presentan en general más riqueza en las fracciones más pequeñas. Comparando bacterias y arqueas, estas últimas presentan menor diversidad y abundancias relativas, pero su relevancia incrementa desde la superficie del océano hacia el batipelágico. Hemos clasificado los grupos taxonómicos bacterianos según si tienen preferencia por fracciones pequeñas, preferencia por fracciones grandes, o si no presentan una preferencia clara por fracciones pequeñas o grandes. Esta clasificación se presenta como una alternativa a la tradicional separación simple entre bacterias de vida libre o asociadas a partículas. La mayoría de gru

We investigated the effects of an increase in dissolved CO2 on the microbial communities of the Mediterranean Sea during two mesocosm experiments in two contrasting seasons: winter, at the peak of the annual phytoplankton bloom, and summer, under low nutrient conditions. The experiments included treatments with acidification and nutrient addition, and combinations of the two. We followed the effects of ocean acidification (OA) on the abundance of the main groups of microorganisms (diatoms, dinoflagellates, nanoeukaryotes, picoeukaryotes, cyanobacteria, and heterotrophic bacteria) and on bacterial activity, leucine incorporation, and extracellular enzyme activity. Our results showed a clear stimulation effect of OA on the abundance of small phytoplankton (pico- and nanoeukaryotes), independently of the season and nutrient availability. A large number of the measured variables showed significant positive effects of acidification in summer compared with winter, when the effects were sometimes negative. Effects of OA were more conspicuous when nutrient concentrations were low. Our results therefore suggest that microbial communities in oligotrophic waters are considerably affected by OA, whereas microbes in more productive waters are less affected. The overall enhancing effect of acidification on eukaryotic pico- and nanophytoplankton, in comparison with the non-significant or even negative response to nutrient-rich conditions of larger groups and autotrophic prokaryotes, suggests a shift towards medium-sized producers in a future acidified ocean

Depending on their relationship with the pelagicc particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to partticles, and are generally separated using only one pore-size filter in a differential filtration. However, particulatte matter in the oceans appears in a continuum of sizes. Here we separated this continuum into 6 discrete size-ffrractions, sized from 0.2 to 200 µm, and described prokaryote diversity in each fraction. Samples were taken in 33 distinct oceanographic projects, which focused on spatial and temporal variability at distinct scales, including dephts of 4,000 m, thus sampling the still poorly-known bathypelagic ocean. Overall, each size frf action presennted different bacterial communities, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larrger particles contribute with new niches. Based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles in which we differentiate the taxonomic groups witth preference for the smaller fractions, tthose that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions. The increase of richness with the size fraction and the preference of some taxa for specific size-fractionns were constant along time, along a coastal-ocean transect and in surface-depth profiles. The only exceptions weere bathypelagic waters (4,000 m), where richness decreased with the size-fraction, something that we associate ttoo the low quality of the organic matter of deep-ocean particles. This special case highlights the particularitty of the bathypelagic ecosystems