Soft Robotic Grippers for Biological Sampling on Deep Reefs

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Abstract

This article presents the development of an underwater gripper that utilizes soft robotics technology to delicately manipulate and sample fragile species on the deep reef. Existing solutions for deep sea robotic manipulation have historically been driven by the oil industry, resulting in destructive interactions with undersea life. Soft material robotics relies on compliant materials that are inherently impedance matched to natural environments and to soft or fragile organisms. We demonstrate design principles for soft robot end effectors, bench-top characterization of their grasping performance, and conclude by describing in situ testing at mesophotic depths. The result is the first use of soft robotics in the deep sea for the nondestructive sampling of benthic fauna.

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Fertile fathoms: Deep reproductive refugia for threatened shallow corals

Daniel Holstein, Tyler Smith, Joanna Gyory … (2015)

The persistence of natural metapopulations may depend on subpopulations that exist at the edges of species ranges, removed from anthropogenic stress. Mesophotic coral ecosystems (30–150 m) are buffered from disturbance by depth and distance, and are potentially massive reservoirs of coral diversity and fecundity; yet we know little about the reproductive capabilities of their constituent species and the potential for these marginal environments to influence patterns of coral reef persistence. We investigated the reproductive performance of the threatened depth-generalist coral Orbicella faveolata over the extent of its vertical range to assess mesophotic contributions to regional larval pools. Over equal habitat area, mesophotic coral populations were found to produce over an order of magnitude more eggs than nearby shallow populations. Positive changes with depth in both population abundance and polyp fecundity contributed to this discrepancy. Relative larval pool contributions of deeper living corals will likely increase as shallow habitats further degrade due to climate change and local habitat degradation. This is a compelling example of the potential for marginal habitat to be critical to metapopulation persistence as reproductive refugia.

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Seasonal Mesophotic Coral Bleaching of Stylophora pistillata in the Northern Red Sea

Orit Nir, David F Gruber, Eli Shemesh … (2014)

Coral bleaching occurs when environmental stress induces breakdown of the coral-algae symbiosis and the host initiates algae expulsion. Two types of coral bleaching had been thoroughly discussed in the scientific literature; the first is primarily associated with mass coral bleaching events; the second is a seasonal loss of algae and/or pigments. Here, we describe a phenomenon that has been witnessed for repeated summers in the mesophotic zone (40–63 m) in the northern Red Sea: seasonal bleaching and recovery of several hermatypic coral species. In this study, we followed the recurring bleaching process of the common coral Stylophora pistillata. Bleaching occurred from April to September with a 66% decline in chlorophyll a concentration, while recovery began in October. Using aquarium and transplantation experiments, we explored environmental factors such as temperature, photon flux density and heterotrophic food availability. Our experiments and observations did not yield one single factor, alone, responsible for the seasonal bleaching. The dinoflagellate symbionts (of the genus Symbiodinium) in shallow (5 m) Stylophora pistillata were found to have a net photosynthetic rate of 56.98–92.19 µmol O2 cm−2 day−1. However, those from mesophotic depth (60 m) during months when they are not bleached are net consumers of oxygen having a net photosynthetic rate between −12.86 - (−10.24) µmol O2 cm−2 day−1. But during months when these mesophotic corals are partially-bleached, they yielded higher net production, between −2.83–0.76 µmol O2 cm−2 day−1. This study opens research questions as to why mesophotic zooxanthellae are more successfully meeting the corals metabolic requirements when Chl a concentration decreases by over 60% during summer and early fall.

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Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)

Shaadi Mehr, Aida Verdes, Rob DeSalle … (2015)

Background The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.

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Author and article information

Journal

Journal ID (nlm-ta): Soft Robot

Journal ID (iso-abbrev): Soft Robot

Journal ID (publisher-id): soro

Title: Soft Robotics

Publisher: Mary Ann Liebert, Inc. (140 Huguenot Street, 3rd FloorNew Rochelle, NY 10801USA )

ISSN (Print): 2169-5172

ISSN (Electronic): 2169-5180

Publication date (Print): 01 March 2016

Publication date PMC-release: 01 March 2016

Volume: 3

Issue: 1

Pages: 23-33

Affiliations

[ ¹ ]Wyss Institute for Biologically Inspired Engineering, Harvard University , Cambridge, Massachusetts.

[ ² ]Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts.

[ ³ ]Department of Ocean Engineering, University of Rhode Island , Narragansett, Rhode Island.

[ ⁴ ]Leon Charney School of Marine Sciences, Haifa University , Haifa, Israel.

[ ⁵ ]Department of Natural Sciences, Baruch College, City University of New York , New York, New York.

[ ⁶ ]American Museum of Natural History, Sackler Institute of Comparative Genomics , New York, New York.

Author notes

Address correspondence to: Robert J. Wood, Charles River Professor of Engineering and Applied Sciences, Harvard John A. Paulson School of Engineering and Applied Sciences Wyss Institute for Biologically Inspired Engineering, Harvard University, 33 Oxford Street, Cambridge, MA 02138, E-mail: rjwood@ 123456seas.harvard.edu

Article

Publisher ID: 10.1089/soro.2015.0019

DOI: 10.1089/soro.2015.0019

PMC ID: 4997628

PubMed ID: 27625917

SO-VID: 9c6e9396-4940-4ddb-b2a2-750d09940a3b

License:

This Open Access article is distributed under the terms of the Creative Commons License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

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Page count

Figures: 17, References: 30, Pages: 11

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