An in situ digital synthesis strategy for the discovery and description of ocean life

Abstract

Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. We present and demonstrate an interdisciplinary approach that uses emerging quantitative imaging technologies, an innovative robotic encapsulation system with in situ RNA preservation and next-generation genomic sequencing to gain comprehensive biological, biophysical, and genomic data from deep-sea organisms. The synthesis of these data provides rich morphological and genetic information for species description, surpassing traditional passive observation methods and preserved specimens, particularly for gelatinous zooplankton. Our approach enhances our ability to study delicate mid-water animals, improving research in the world’s oceans.

Transcriptome sequencing of seven deep marine invertebrates

“…In August 2021, a ten-day integrated expedition aboard the Schmidt Ocean Institute’s R/V Falkor was conducted on the Pacific Ocean off the coast of San Diego, CA 3 . The expedition involved seven dives of the remotely operated vehicle (ROV) SuBastian, each lasting approximately eight hours.…”

“… The EyeRIS plenoptic camera system, which enables 3D imaging and tracking of marine life. The rotary actuated dodecahedron (RAD-2) for specimen encapsulation and tissue sampling 3 , 9 . RAD-2 is a 12-sided encapsulation device that uses a rotary actuator to open and close.…”

“…Gelatinous animals of the midwater harbour novel biology that can be unveiled through 3D modelling and whole genome and transcriptome sequencing 3 . They offer vital ecosystem services, establishing connections to the global food web, fisheries, and carbon sequestration in the deep sea, but estimates from the deep sea are lacking 4 .…”

“…The combination of whole transcriptomic genetic data coupled with high quality qualitative and quantitative image data allows for in depth exploration of the biology and evolution of deep-sea animals 3 . Here we present image and whole transcriptome data for 7 deep sea gelatinous animals (Fig.…”

“…Here we present image and whole transcriptome data for 7 deep sea gelatinous animals (Fig. 1 ) that were collected as part of a research project that involved development of new technologies and elaboration of an integrated workflow to capture in situ image and genetic data from delicate gelatinous zooplankton 3 . The animals include 3 siphonophores: Praya sp., Apolemia sp., and Halistemma sp.…”