Key advances: global plankton morphometrics, carbon export proxies, EcoTaxa
Complementing omics approaches, Tara Oceans deployed a suite of automated and high‑resolution imaging technologies to quantify plankton abundance, morphology, and size structure across trophic levels. These included the Underwater Vision Profiler, ZooScan, FlowCAM, Imaging FlowCytobot, flow cytometry, and a dedicated 3D high‑content fluorescence microscopy pipeline (Table 2). Together, these methods covered organisms from picoplankton to large gelatinous zooplankton and marine aggregates, from the surface to 1,000 m depth (Tara Oceans publication numbers 34, 60, 67, 78, 93, 121).
More than six million plankton images have been generated and expert‑validated, representing one of the largest curated environmental imaging datasets worldwide. To enable community annotation and data sharing, the consortium developed EcoTaxa, a web‑based platform for collaborative image classification supported by machine‑learning tools (https://ecotaxa.obs-vlfr.fr/). EcoTaxa is interoperable with the WoRMS eukaryotic taxonomy framework, facilitating direct integration of imaging and sequencing data.
Tara Oceans imaging data have been instrumental in revealing plankton interactions, validating ecological networks inferred from omics, quantifying carbon export pathways, and uncovering the unexpectedly large biomass contribution of previously overlooked protist groups (Tara Oceans publication numbers 25, 34, 38, 118, 135, 145). The combined morpho‑genetic resources from the project represent a veritable treasure trove providing a foundation for future studies in ecology, evolution, and comparative cell biology.
Table 2. Key features, size, and completion of imaging datasets generated from >9 200 plankton samples collected by the Tara Oceans (TO) and Tara Oceans Polar Circle (TOPC) expeditions.
| Imaging dataset (Instrument & plankton samples) | Plankton size range | Voyage | # of plankton samples analysed | Sample imaging & processing | # objects | Classification (predicted P, curated C) | EcoTaxa Release |
|---|---|---|---|---|---|---|---|
| UVP | 100 > 1 mm | TO + TOPC | 776 | 100% | 769 497 | P + C (100%) | available |
| ZooScan 680 Regent | 100 > 0.68 mm | TO | 189 | 100% | 126 389 | P + C (36%) | available |
| ZooScan WP2 200 | 10 > 0.2 mm | TO + TOPC | 203 | 100% | 394 956 | P + C (95%) | available |
| ZooScan Multinet | 10 > 0.2 mm | TO | 285 | 100% | 397 723 | P + C (92%) | available |
| ZooScan Bongo 300 | 10 > 0.3 mm | TO | 92 | 100% | 154 624 | P + C (30%) | available |
| ZooScan 680 Regent | 10 > 0.68 mm | TOPC | 23 | 100% | 14 433 | P + C (16%) | available |
| ZooScan Bongo 300 | 10 > 300 µm | TOPC | 19 | 100% | 42 365 | P + C (8%) | available |
| FlowCAM 180 Bongo | 180 > 20 µm | TOPC | 317 | 100% | 704 053 | P + C (15%) | available |
| IFCB | 160 > 5 µm | TOPC | 6982 | 100% | 2 307 437 | P + C (30%) | available |
| e-HCFM H5 5-20 | 20 > 5 µm | TO | 76 | 100% | 336 655 | P + C (5,5%) | available |
| e-HCFM H20 20-180 | 180 > 20 µm | TO + TOPC | 128 | 100% | >106 | – | 2017 |
| e-HCFM H0.2 >0.2 | 0.2 µm | TOPC | 14 | 100% | – | 2017 | |
| HiRes 3D-CLSM | 2000 > 1 µm | TO | 65 | 50% | 3 551 | C (100%) | 2017 |
| SEM | 200 > 0.1 µm | TO | 31 | STEFIexp | 427 | C (100%) | 2017 |
| TEM virus | < 0.1 µm | TO + TOPC | 43 | 100% | 4300 | C (100%) | 2017 |
| TOTAL | 9243 | 6 million |