Niche adaptation promoted the evolutionary diversification of tiny ocean predators

Latorre, Francisco; Deutschmann, Ina Maria; Labarre, Aurélie; Obiol, Aleix; Krabberød, Anders K.; Pelletier, Éric; Sieracki, Michael E.; Cruaud, Corinne; Jaillon, Olivier; Massana, Ramón; Logares, Ramiro

doi:10.1073/pnas.2020955118

Cited by 17 publications

(29 citation statements)

References 99 publications

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“…Thus, if the study aim is to explore patterns of network topology rather than single edges, inferring a network comparable to the real interaction network may be more useful than accuracy of single edges. However, investigations aiming to provide potential interaction partners may use EnDED with the intersection combination approach (e.g., [ 51 ]). Specific associations may be validated with experiments or microscopy [ 6 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

Disentangling environmental effects in microbial association networks

et al. 2021

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Background Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. Results We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges—87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. Conclusions To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses.

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Section: Discussionmentioning

confidence: 99%

Disentangling environmental effects in microbial association networks

et al. 2021

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“…In global studies with strong latitudinal gradients, temperature has a marked effect in most planktonic groups (Ibarbalz et al 2019), and HF assemblages are not an exception (Patterson and Lee 2000; Azovsky et al 2016). The temperature effect was also detected in studies targeting specific HF taxa (Boenigk et al 2006; Rodríguez‐Martínez et al 2013; Flegontova et al 2020; Latorre et al 2021). Despite samples analyzed here having a relatively narrow temperature range (16–29°C), we could detect a temperature effect on HF assemblages, highlighting the possible alterations that these could face by the expected increase of sea surface temperature due to global warming (Hutchins and Fu 2017).…”

Section: Discussionmentioning

confidence: 79%

Oceanic heterotrophic flagellates are dominated by a few widespread taxa

Obiol

Muhovic

Massana

2021

Limnology & Oceanography

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Marine heterotrophic flagellates (HFs) form a diverse and ecologically relevant functional group of bacterial grazers and nutrient remineralizers in oceanic waters. Despite playing a crucial role in marine biogeochemical cycles, there is still a lack of information on which specific taxa dominate HF assemblages and what are their patterns of distribution in a global context. In the present work, we addressed this issue by analyzing amplicon sequencing data sets retrieved from samples taken in tropical and subtropical oceanic regions at depths from surface to 4000 m. Only a few dozens of widespread taxa, mostly affiliating to MAST clades, Picozoa, Bicosoecida and Chrysophyceae, seemed to dominate surface HF assemblages. The majority of these dominant HFs were present at relatively constant abundances, while others were influenced by temperature or displayed a patchy distribution. In the deep ocean, only a handful of taxa belonging to Bicosoecida and Chrysophyceae, together with Diplonemea and Kinetoplastida, explained most of the HF signal. Co‐occurrence networks between HF and prokaryotic taxa at the surface ocean revealed two main clusters influenced by temperature that did not seem to show specific patterns of interaction. However, some correlations emerged outside these thermal groups that could represent new prey–predator interactions. Overall, we identified the putatively most ecologically relevant HF taxa in the ocean, which become promising targets for further experimental and genomic studies.

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“…They are responsible for ~50% of annual planktonic photosynthetic primary productivity (PP), of which they consume ~66%, plus an additional 10% of bacterial PP (Calbet and Landry, 2004;Steinberg and Landry, 2017). Recent applications of molecular tools such as metabarcoding (de Vargas et al, 2015;Choi et al, 2020), metagenomics and single cell genomics (Latorre et al, 2021), have significantly sharpened our understanding of protist diversity, distributions, and functionality, from basic trophic modes to complex metabolic pathways, and emphasized their importance in channeling marine productivity to upper trophic levels. The available observational data is rich in horizontal spatial and temporal coverage, yet lacks vertical resolution, particularly below the photic zone (Ollison et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The protist community traces seasonality and mesoscale hydrographic features in the oligotrophic Sargasso Sea

et al. 2022

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Protists represent the majority of the eukaryotic diversity in the oceans. They have different functions in the marine food web, playing essential roles in the biogeochemical cycles. While the available data is rich in horizontal and temporal coverage, little is known on their vertical structuring, particularly below the photic zone. The present study applies V4 18S rDNA metabarcoding to samples collected over three years in conjunction with the BATS time-series to assess marine protist communities in the epipelagic and mesopelagic zones (0-1000 m). The protist community showed a dynamic seasonality in the epipelagic, responding to hydrographic yearly cycles. Mixotrophic lineages dominated throughout the year. However, autotrophs bloomed during the rapid transition between the winter mixing and the stratified summer, and heterotrophs had their peak at the end of summer, when the base of the thermocline reaches its deepest depth. Below the photic zone, the community, dominated by Rhizaria, is depth-stratified and relatively constant throughout the year, although they followed local hydrographic and biological features such as the oxygen minimum zone. The results suggest a dynamic partitioning of the water column, where the niche vertical position for each community changes throughout the year in the epipelagic, likely depending on nutrient availability, the mixed layer depth, and other hydrographic features. At depth, the protist community closely tracked mesoscale events (eddies), where the communities followed the hydrographic uplift, raising the deeper communities for hundreds of meters, and compressing the communities above.

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Niche adaptation promoted the evolutionary diversification of tiny ocean predators

Cited by 17 publications

References 99 publications

Disentangling environmental effects in microbial association networks

Disentangling environmental effects in microbial association networks

Oceanic heterotrophic flagellates are dominated by a few widespread taxa

The protist community traces seasonality and mesoscale hydrographic features in the oligotrophic Sargasso Sea

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