Modelling plankton ecosystems in the meta-omics era. Are we ready?

Stec, Krzysztof; Caputi, Luigi; Buttigieg, Pier Luigi; D’Alelio, Domenico; Ibarbalz, Federico M.; Sullivan, Matthew B.; Chaffron, Samuel; Bowler, Chris; d’Alcalà, Maurizio Ribera; Iudicone, Daniele

doi:10.1016/j.margen.2017.02.006

Cited by 30 publications

(29 citation statements)

References 227 publications

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“…The future of marine communities' modeling lies in the integration of omics datasets into modeling frameworks [18,[70][71][72][73]. The use of metabolic networks and gene-centric methods has already shown very promising results in modeling prokaryotic ecological dynamics [18,73].…”

Section: Towards An Integration Of Mixotrophic Diversity Into Marine mentioning

confidence: 99%

“…The use of metabolic networks and gene-centric methods has already shown very promising results in modeling prokaryotic ecological dynamics [18,73]. However, eukaryotic metabolic complexity makes these methods hard to apply on protists for now, and we still lack a universal theoretical framework on how to integrate such methods into concrete modeling [70]. Mixotrophic protists are physiologically complex, and their feeding behavior can vary drastically on short time scales [9].…”

Section: Towards An Integration Of Mixotrophic Diversity Into Marine mentioning

confidence: 99%

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Mixotrophic protists display contrasted biogeographies in the global ocean

et al. 2019

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Mixotrophy, or the ability to acquire carbon from both auto-and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.

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Section: Towards An Integration Of Mixotrophic Diversity Into Marine mentioning

confidence: 99%

Section: Towards An Integration Of Mixotrophic Diversity Into Marine mentioning

confidence: 99%

Mixotrophic protists display contrasted biogeographies in the global ocean

et al. 2019

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“…In fact, most of the issues discussed in this paper were stimulated by the observations conducted over the last decades at the LTER station MC in the bay of Napoli (Zingone et al 2019). This information, especially if integrated with modern techniques and approaches, especially those based on bioptical and molecular methods, can feed a new generation of models (Coles et al 2017, Stec et al 2017.…”

Section: What Knowledge Gaps Do We Have To Fill and How Could They Bementioning

confidence: 98%

Similarities, differences and mechanisms of climate impact on terrestrial vs. marine ecosystems

d’Alcalà¹

2019

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Comparisons between terrestrial and marine ecosystems are generally not in the main stream of scientific literature even though Webb (2012) listed several points for which the transfer of knowledge and concepts related to one or to the other system would benefit our understanding of both. Even sharing this view, the leading hypothesis behind this contribution is that the pelagic system, where the dominant biotic component by number and biomass is microscopic, has specific features which strongly differentiate it from the above-the-surface terrestrial systems. Due to this, climate change, i.e. changes in temperature, precipitation and most importantly in the dynamics of the two fluid media, atmosphere and ocean, act with different mechanisms which prevents proceeding with analogies in many cases. In addition, the non-linearity of most of the processes and responses to perturbations requires, in order to obtain reliable forecasts or hindcasts, a detailed analysis of the path followed by the system which is normally overlooked in the step-change simulations or projections.

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“…However, the incorporation of omics information in global ocean models poses several challenges (i) because a conceptual framework (Figure 9) is still lacking for fully integrating omics knowledge into plankton ecosystem models (Stec et al, 2017) and (ii) because the number of omics-based biomarkers often remains too large to be directly incorporated as proper variables into ocean models (Tréguer et al, 2018). It is thus necessary to establish a roadmap toward fully integrated observations and their inclusion into operational tools.…”

Section: Toward Holistic Marine Ecosystems Monitoring For Improving Omentioning

confidence: 99%

Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

et al. 2019

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Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes Frontiers in Marine Science | www.frontiersin.org 1 October 2019 | Volume 6 | Article 623 Capotondi et al. Marine Ecosystems Modeling and Forecastinginvolved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.

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Modelling plankton ecosystems in the meta-omics era. Are we ready?

Cited by 30 publications

References 227 publications

Mixotrophic protists display contrasted biogeographies in the global ocean

Mixotrophic protists display contrasted biogeographies in the global ocean

Similarities, differences and mechanisms of climate impact on terrestrial vs. marine ecosystems

Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

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