“Why Study Biology by the Sea?” (University of Chicago Press, 2020) is a fascinating collection of essays on the historical emergence of marine biological stations, the diversity of work they pursue, and their significant contributions to scientific discovery and knowledge.
The volume sprang from discussions at the 29th annual MBL-ASU History of Biology Seminar at the Marine Biological Laboratory (MBL) in 2016, organized by Jane Maienschein of Arizona State University and Karl Matlin of University of Chicago.
Several essays explore MBL history, including a profile of the seaside lab that inspired its formation (the Stazione Zoologica in Naples, Italy) and the MBL's inspiration, in turn, of the first marine lab in China. Bookending the volume are a foreword by MBL Director Nipam Patel and an epilogue by Alejandro Sánchez Alvarado of the Stowers Institute, both of which situate the MBL in the present day.
As essays on the MBL’s early years reveal, the lab remains remarkably true, in many respects, to the ethos on which it was founded. The MBL’s first director, C.O. Whitman, felt strongly that the lab's scientific integrity depended on integrating research and education, a topic MBL McDonnell Fellow Kate MacCord explores in the book. (Whitman even fended off a proposed merger with the Carnegie Institution during a dire period in MBL’s financial history, MacCord writes, because a condition of the merger was scuttling the MBL’s educational mission.) And in an era of increasing specialization in biology, Whitman firmly believed the lab should investigate a wide diversity of organisms and questions, a strategy that both Patel and Sánchez Alvardo pick up as being essential today, with particular reference to marine biodiversity.
In “Microscopes and Moving Molecules: The Discovery of Kinesin at the MBL,” Matlin probes how a culture of intense collaboration and competition at the MBL, along with new, enabling technologies in light microscopy, played crucial roles in a major new finding. In another essay, MBL McDonnell Scholar Kathryn Maxson Jones focuses on research using the squid giant axon in the 1940s and 1950s, including at the MBL. Her essay, writes Fabio De Sio in a review of the volume, argues for “the importance of marine stations for the birth of the neurosciences, as frameworks for novel experimental systems, and as niches for the cultivation in parallel of both model-based and comparative approaches."
Both longtime fans and new members of the MBL community will find much to discover in “Why Study Biology By the Sea?” The volume, co-edited by Matlin, Maienschein, and Rachel A. Ankeny, is available for purchase through the MBL Gift Shop.
This book is the third volume in a series edited by Maienschein called "Convening Science: Discovery at the Marine Biological Laboratory." The next volume, "Nature Remade: Engineering Life, Envisioning Worlds," will be published in July 2021.
Contact: Diana Kenney
dkenney@mbl.edu; 508-605-3525
By Alison Caldwell
University of Chicago Medicine
Study suggests plaque may have been a “stepping stone” for microbes into the body
Alon Shaiber of Cornell Weill Medicine, left, and A. Murat Eren (Meren) of University of Chicago and the MBL. Photo courtesy of Meren.
“Not only is it the beginning of the GI tract, but it’s also a very special and small environment that’s microbially diverse enough that we can really start to answer interesting questions about microbiomes and their evolution,” said Eren, an assistant professor in the Department of Medicine at the University of Chicago and an MBL Fellow at the UChicago-affiliated Marine Biological Laboratory (MBL), Woods Hole.
“There’s a surprising amount of site specificity, in that you find defined patterns of microbes in different areas of the mouth — the microbes associated with the tongue are very different from those on the plaque on your teeth,” he continued. “Your tongue microbes are more similar to those living on someone else’s tongue than they are to those living in your throat or on your gums!”
In a pair of papers published on Dec. 16 in Genome Biology, Eren, who goes by Meren, and colleagues, including senior co-author and MBL Associate Scientist Jessica Mark Welch, zeroed in on this unique ecology with state-of-the-art sequencing and analysis approaches to get a better picture of the oral microbiome.
Their approach involved analyzing the genomes of all the microbes in each oral cavity environment they tested.
“Normally when we study a microbial environment, we take samples and only read a small fraction of the genomes present — just enough to ID the broad categories of microbes,” said Meren. “We used a more comprehensive approach called metagenomics, which allowed us to sequence the entire DNA content of our samples from the oral cavity. We were able to reconstruct entire microbial genomes, identifying new microbial species and figuring out where each one fits on the tree of life.”
In one paper (Utter et al.), the researchers studied the microbial residents of three distinct parts of the mouth, providing insight into population structure and spatial arrangement of the oral microbiome and forming hypotheses about adaptation to specific habitats. In the second paper (Shaiber et al.), they focused on one particularly difficult-to-study class of bacteria: Saccharibacteria (TM7). Their results have surprising implications for the evolution of microbes in the mouth.
Different TM7 species could be grouped into six distinct bins, or clades, they found, based the similarities of their genomes, which indicate how recently the different species split from one another in their evolutionary history.
When the team compared those bins to other groups of TM7 species, like those found in the environment outside of the body or in human or animal guts, they were amazed to find that, genetically, instead of the plaque and tongue TM7 species grouping together, the TM7 species from dental plaque grouped more closely with the TM7 species found in soil, while the TM7 species on the tongue more closely resembled those found in the gastrointestinal tract.
“The first time I plotted the phylogeny comparing the TM7 of the tongue and plaque and saw that they were completely separate, my mind exploded,” said first author Alon Shaiber, now a genomics data scientist at Weill Cornell Medicine. “We did not expect that at all.”
MBL Associate Scientist Jessica Mark Welch in an MBL teaching lab with University of Chicago students. Credit: Ege Yalcindag
“This was the most exciting thing to us,” he continued. “This shows that the dental plaque, the enemy of our health that we constantly try to get rid of, may at some point have played an important role in the evolution of some of the microbes to call our bodies their home.”
The metagenomics approach meant that the researchers could identify new species of bacteria from the oral cavity that had not previously been studied, due to the challenges of cultivating some of these microbes in the lab.
“The mouth is so easily accessible that people have been working on bacteria from the mouth for a long time,” said Jessica Mark Welch. “But we’re finding that there are entire new microbial groups, including a few really weird and unusual ones, that have not been looked at before.”
Beyond its utility for understanding the evolution and composition of the microbiome, this study and others like it can provide new insights on the role of oral microbes in human health.
“Every environment we look at has these really complicated, complex communities of bacteria, but why is that?” said Mark Welch. “Understanding why these communities are so complex and how the different bacteria interact will help us better understand how to fix a bacterial community that’s damaging our health, telling us which microbes need to be removed or added back in.”
Future research will be aimed at teasing apart the genetic and functional relationships between these newly identified bacterial species, especially in categories of bacteria other than TM7, and how these microbial communities play a role in human biology and disease. The metagenomics approach will also prove useful for studying microbial communities in other places, such as the gut and in environmental settings.
“These kinds of studies are showing us the diversity in the mouth in a new way,” said Mark Welch. “We’re learning about exactly what genes are in different microbes, which will make it possible to model the metabolism of entire communities. The bacteria in the mouth are really a microcosm of ecology, and it relates to the ecology you see at a landscape scale all around us.”
Homepage photo: Bacterial biofilm scraped from the surface of the tongue and imaged using CLASI-FISH. Credit: Steven Wilbert and Gary Borisy, The Forsyth Institute
Citations:
Daniel R. Utter, G. G. Borisy, C.M. Cavanaugh, and J.L. Mark Welch (2020) Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biology, DOI: 10.1186/s13059-020-02200-2
Alon Shaiber, A.D. Willis, T.O. Delmont, S. Roux, L-X Chen, A.C. Schmid, M. Yousef, A.R. Watson, K. Lolans, O.C. Esen, S.T.M. Lee, N. Downey, H.G. Morrison, F.E. Dewhirst, J.L. Mark Welch, and A.M Eren (2020) Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biology, DOI: 10.1186/s13059-020-02195-w
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
Contact: dkenney@mbl.edu; 508-685-3525
WOODS HOLE, Mass. – It sounds like a “Just So Story” – “How the Insect Got its Wings” – but it’s really a mystery that has puzzled biologists for over a century. Intriguing and competing theories of insect wing evolution have emerged in recent years, but none were entirely satisfactory. Finally, a team from the Marine Biological Laboratory (MBL), Woods Hole, has settled the controversy, using clues from long-ago scientific papers as well as state-of-the-art genomic approaches. The study, conducted by MBL Research Associate Heather Bruce and MBL Director Nipam Patel, is published this week in Nature Ecology & Evolution.
Insect wings, the team confirmed, evolved from an outgrowth or “lobe” on the legs of an ancestral crustacean (yes, crustacean). After this marine animal had transitioned to land-dwelling about 300 million years ago, the leg segments closest to its body became incorporated into the body wall during embryonic development, perhaps to better support its weight on land. “The leg lobes then moved up onto the insect’s back, and those later formed the wings,” says Bruce.
Injection of CRISPR solution into crustacean embryos (Parhyale hawaiensis). Credit: Heather Bruce
Heather Bruce dissecting crustacean embryos, wearing an arthropod shirt of her own design. Credit: Eric Chen
One of the reasons it took a century to figure this out, Bruce says, is that it wasn’t appreciated until about 2010 that insects are most closely related to crustaceans within the arthropod phylum, as revealed by genetic similarities.
“Prior to that, based on morphology, everyone had classified insects in the myriapod group, along with the millipedes and centipedes,” Bruce says. “And if you look in myriapods for where insect wings came from, you won’t find anything,” she says. “So insect wings came to be thought of as ‘novel’ structures that sprang up in insects and had no corresponding structure in the ancestor -- because researchers were looking in the wrong place for the insect ancestor.”
“People get very excited by the idea that something like insect wings may have been a novel innovation of evolution,” Patel says. “But one of the stories that is emerging from genomic comparisons is that nothing is brand new; everything came from somewhere. And you can, in fact, figure out from where.”
Insects incorporated two ancestral crustacean leg segments (labeled 7 in red and 8 in pink) into the body wall. The lobe on leg segment 8 later formed the wing in insects, while this corresponding structure in crustaceans forms the tergal plate. Credit: Heather Bruce
Bruce picked up the scent of her now-reported discovery while comparing the genetic instructions for the segmented legs of a crustacean, the tiny beach-hopper Parhyale, and the segmented legs of insects, including the fruit fly Drosophila and the beetle Tribolium. Using CRISPR-Cas9 gene editing, she systematically disabled five shared leg-patterning genes in Parhyale and in insects, and found those genes corresponded to the six leg segments that are farthest from the body wall. Parhyale, though, has an additional, seventh leg segment next to its body wall. Where did that segment go, she wondered? “And so I started digging in the literature, and I found this really old idea that had been proposed in 1893, that insects had incorporated their proximal [closest to body] leg region into the body wall,” she says.
“But I still didn’t have the wing part of the story,” she says. “So I kept reading and reading, and I came across this 1980s theory that not only did insects incorporate their proximal leg region into the body wall, but the little lobes on the leg later moved up onto the back and formed the wings. I thought, wow, my genomic and embryonic data supports these old theories.”
It would have been impossible to resolve this longstanding riddle without the tools now available to probe the genomes of a myriad of organisms, including Parhyale, which the Patel lab has developed as the most genetically tractable research organism among the crustaceans.
Parhyale hawaiensis, shown here eating, has had its genome sequenced and is the most genetically tractable crustacean for biological research.
Credit: Heather Bruce
Citation: Heather S. Bruce and Nipam H. Patel (2020) Knockout of crustacean leg patterning genes suggests that insect wings and body wall evolved from ancient leg segments. Nature Ecol. Evol., DOI: 10.1038/s41559-020-01349-0
Download a copy of the paper here.
Homepage photo: An azure hawker dragonflly alights. Credit: Wikimedia
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
Contact: dkenney@mbl.edu; 508-685-3525
An octopus (O. bimaculoides) extends an arm to explore its environment. Credit: Michael LaBarbera
Amazingly, all eight arms could perform all four types of deformation (bend, twist, elongate, shorten) throughout their length. Moreover, each type of movement could be deployed in multiple orientations (e.g. left, right, up, down, 360º, etc.). Especially noteworthy was the clockwise and counterclockwise twisting that could occur throughout each arm during bending, shortening or elongating. This twisty strong arm is exceptionally flexible by any standard.
“Even our research team, which is very familiar with octopuses, was surprised by the extreme versatility of each of the eight arms as we analyzed the videos frame-by-frame,” said co-author and MBL Senior Scientist Roger Hanlon. “These detailed analyses can help guide the next step of determining neural control and coordination of octopus arms, and may uncover design principles that can inspire the creation of next-generation soft robots.”
Engineers have long wished to design “soft robotic arms” with greater agility, strength and sensing capability. Currently, most robotic arms require hard materials and joints of many configurations, all of which have limitations. The octopus presents a novel model for future robotic designs. Octopus arms are similar in function to the human tongue and the elephant trunk; they are muscular hydrostats that use incompressible muscle in different arrangements to produce movement. The current study provides a basis for investigating motor control of the entire octopus arm. Soft, ultra-flexible robotic arms could enable many new applications, e.g., inspecting unstructured and cluttered environments such as collapsed buildings, or gentler medical inspection of alimentary or respiratory pathways.
Examples of arm deformation types in an octopus (O. bimaculoides). Credit: Roger Hanlon Laboratory/Marine Biological Laboratory
Citation: E.B. Lane Kennedy, Kendra C. Buresch, Preethi Boinapally, and Roger T. Hanlon (2020) Octopus Arms Exhibit Exceptional Flexibility. Scientific Reports, DOI: 10.1038/s41598-020-77873-7
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
Ctenophore Pleurobrachia with ctenes (along left side of body) at different stages of their power stroke.
The study, published in Scientific Reports, found that small marine animals with multiple propulsers—including larval crabs, polychaete worms, and some types of jellyfish—don’t push themselves forward when they move their appendages, but instead create negative pressure behind them that pulls them through the water.
When the front appendage moves, it creates a pocket of low pressure behind it that may reduce the energy required by the next limb to move. “It is similar to how cyclists use draft to reduce wind drag and to help pull the group along,” says lead author Sean Colin of Roger Williams University, a Whitman Center Scientist at the MBL.
This publication builds on the team’s previous work, also conducted at the MBL, on suction thrust in lampreys and jellyfish. For the current study, they focused on small marine animals that use metachronal kinematics also known as “metachronal swimming,” a locomotion technique commonly used by animals with multiple pairs of legs in which appendages stroke in sequence, rather than synchronously.
“We came into this study looking for the benefits of metachronal swimming, but we realized the flow around the limbs looks very similar to the flow around a jellyfish or a fish fin,” said Colin. “Not only does the flow look the same, but the negative pressure is the same.”
For this study, the researchers worked with two crab species, a polychaete worm, and four species of comb jellies. All are smaller than a few millimeters in length. They found that the fluid flow created while swimming was the same as in the larger animals they had previously studied.
“Even at these really small scales, these animals rely on negative pressure to pull themselves forward through the water,” said Colin, who added that this could be a common phenomenon among animals.
“It’s not unique to the fish or the jellyfish we looked at. It’s probably much more widespread in the animal kingdom,” says Colin, who added that something like suction thrust has been observed in birds and bats moving themselves through the air. These creatures have the same degree of bend in their limbs (25-30 degrees) that the observed marine animals do.
Video by Emily Greenhalgh, MBL
Moving forward, Colin and colleagues want to study a larger variety of marine organisms to determine the range of animal sizes that rely on suction thrust to propel through the water.
“That’s one of our main goals -- to get bigger, get smaller, and get a better survey of what animals are really relying on this suction thrust,” Colin says.
Colin’s MBL Whitman Center collaborators on this study include John Costello of Providence College and John O. Dabiri of California Institute of Technology. Previous research on lampreys was conducted in collaboration with MBL Senior Scientist Jennifer Morgan.
Citation: Colin, S.P., Costello, J.H., Sutherland, K.R., Gemmel, B.J., Dabiri, J.O. and Du Clos, K.T. (2020) The role of suction thrust in the metachronal paddles of swimming invertebrates. Scientific Reports, DOI: 10.1038/s41598-020-74745-y
Polychaete worm, Tomopteris, with setae moving on each side of the body in metachronal waves
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
The MBL offers immersive courses, workshops, and conferences year-round. Central to the MBL’s identity are its advanced, discovery-based courses for graduate students, postdoctoral fellows, and faculty. READ MORE >
MBL scientists pursue research in diverse areas of fundamental biological discovery, to explore the origins, diversity, and nature of life on a changing planet and to inform the human condition. READ MORE >
The MBL’s convening power attracts the world’s most accomplished scientists to Woods Hole to carry out some of their most creative and far-reaching work. READ MORE >
The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.