Novel underwater microscope brings the lab to the ocean

Benthic Underwater Microscope

Coral life through the eyes of a seafloor imaging system.

The kiss, the war and the invasion of corals.

A new underwater microscope is bringing to the surface never-before-seen images of seafloor organisms. Researchers from Scripps Institution of Oceanography at the University of California San Diego designed and developed a novel diver-operated underwater microscope. It collects microscopic images with micrometer resolution of benthic organisms such as corals and is named Benthic Underwater Microscope (BUM).

Benthic Underwater Video, Coral, Stylophora Benthic Underwater Video, Coral Benthic Underwater Video, Coral, Pocillopora

In situ image of the coral Stylophora and Pocillopora| In situ images acquired using the 3x/5x objective lens. The image is an enhanced depth of field (DOF) composite formed from a focal scan z-stack. Credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego

Microscope_LabImage6 - Stylophora - 1.7x1.4_FOV - Fluorescence

Who developed this novel underwater microscope: Benthic Underwater Microscope (BUM)?

The Jaffe Lab from Scripps Institution of Oceanography at the University of California has a history in designing a variety of systems for acquiring microscopic images. Dr. Jules Jaffe, the principle investigator of the lab and its team recognised the important deficiency in the ability to observe the natural marine environment. Hence, by using their knowledge and past experience on plankton imaging systems they developed the Benthic Underwater Microscope (BUM). Specifically, Mr. Andrew Mullen (PhD student) and Dr. Tali Treibitz (Post-doc) worked for one and a half years to bring the idea of BUM to its use in the ocean.

What are the special features and benefits of this novel underwater microscope?

Andrew Mullen, co-lead author of the study published in the journal Nature Communications said: “This underwater microscope is the first instrument to image the seafloor at such small scales and the system is capable of seeing features as small as single cells underwater”.

The Benthic Underwater Microscope (BUM) is the first systems that can collect microscopic images of organisms on the seafloor with nearly micrometer resolution.  It is the first time that scientists obtain this microscopic view of organisms on the seafloor. Benthic Underwater MicroscopThe captured images offer powerful means for scientists to investigate new questions about marine organisms and the environment. The entire system is custom designed and built. As a result, one of the major benefits of BUM is that it is portable, records processes of seafloor organisms with minimal disturbance to the organisms itself and their surrounding environment. Before BUM scientists had to collect samples from the field and bring them back to lab for obtaining micro-scale images and studying the seafloor organisms.

Positioning of the Benthic Underwater Microscope by Scripps Oceanography PhD Student Andrew Mullen. Credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego

The kiss, the war and the invasion of corals.

What did the scientists discover?

The novel underwater microscope system was tested in Red Sea (Israel) in Maui (Hawaii) where they captured coral behavior, took images on coral bleaching and algae invasion. Assistance in the coral reefs studies and the instrument application was provided by Dr. Emily Kelly and Dr. Jennifer Smith (Maui study); as well as Dr. Rael Horwitz and Dr. Amatzia Genin (Red Sea study).

The research team has now records the activity of coral polyps, to investigate coral-coral turf wars and the colonization of bleached corals by microscopic algae.

They captured the coral ‘polyp kissing’, a periodically embracing of neighboring corals throughout the night during their investigation in the Red Sea. “We were definitely surprised by this interesting behavior, and we are not completely sure of its purpose” the scientists say and they guess that this ‘kissing’ might be means of exchanging organic materials between coral polyps.

Polyp kissing




Coral ‘polyp kissing’ Periodic interactions between adjacent Stylophora coral polyps involving the touching of their gastrovascular cavity openings. Credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego

Coral-coral competition is well-studied field. However the research team examined the coral-coral turf wars with the use of BUM. Thus enabled to observe the dynamics of coral competition in the natural environment at such a small scale for the first time. The videos revealed that corals are able to determine friend from foe: different colonies of the same species did not show any aggressive behavior when placed next to each other compared to colonies of different species.

Underwater Microscopy, Coral competition, Platygyra, Stylophora




Coral Competition | In situ image of competition between the corals Platygyra (left) and Stylophora (right) recorded in situ. The field of view is 17 x 14 mm. Credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego


Algal invasion in terms of overgrowth can drastically change Benthic Underwater Microscopy, Macrolagae, growth, coral, invasionthe health and structure of the reef. By using BUM the research team is now able to give insight into the invasion process of bleached corals by filamentous algae. Furthermore, they recorded a previously unreported honeycomb pattern of initial algal colonization and growth in areas between the individual coral polyps during coral bleaching. Captured pictured showed that during bleaching events algae are able to actively overgrow living corals.

Coral Invasion By Algae | Bleached Porities coral colony being colonized and overgrown by turf algae. Credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego


What is the potential use for other research topics?

The BUM system has potential to be used for studying a wide variety of important marine ecosystems and questions. Most noteworthy is that besides the broad range of topics related to corals reefs, other ecosystems could be investigated:  kelp forests, rocky reefs, sea grass beds, and mangroves. Additionally, it could be used in the field of biofouling studies that has a significant scientific and economical value, as industry and human health is directly related to it. Therefore, the research team hopes “to both improve the instrument’s current capabilities as well as incorporated the ability to measure additional parameters” that will have the potential to facilitate wide usage of the system by the scientific community.

The BUM system brings the lab to the ocean, instead of bringing the ocean to the lab. This novel underwater microscope enables to observe and investigate the natural processes in their real environment. To protect better our marine environments we need to better understand the small-scale processes that influence these ecosystems. The novel underwater microscope BUM is one big step towards it.


STORY SOURCE:  The above post is written based on materials published by Nature and materials provided by the authors. Note: Materials may be edited for content and length.
PICTURE  SOURCE:  Image credit: Jaffe Lab for Underwater Imaging, Scripps Institution of Oceanography at UC San Diego
CITE THIS PAGE: “Novel microscope brings the lab to the ocean?” The Blue Reporters, July 2016.  
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