450-million-year-old organism finds new life in Softbotics

Researchers in the Department of Mechanical Engineering at Carnegie Mellon University, in collaboration with paleontologists from Spain and Poland, used fossil evidence to engineer a soft robotic replica of pleurocystitid, a marine organism that existed nearly 450 million years ago and is believed to be one of the first echinoderms capable of movement using a muscular stem.

Published today in The Proceedings of the National Academy of Science (PNAS), the research seeks to broaden modern perspective of animal design and movement by introducing a new a field of study -- Paleobionics -- aimed at using Softbotics, robotics with flexible electronics and soft materials, to understand the biomechanical factors that drove evolution using extinct organisms.

"Softbotics is another approach to inform science using soft materials to construct flexible robot limbs and appendages. Many fundamental principles of biology and nature can only fully be explained if we look back at the evolutionary timeline of how animals evolved. We are building robot analogues to study how locomotion has changed," said Carmel Majidi, lead author and Professor of Mechanical Engineering at Carnegie Mellon University.

With humans' time on earth representing only 0.007% of the planet's history, the modern-day animal kingdom that influences understanding of evolution and inspires today's mechanical systems is only a fraction of all creatures that have existed through history.

Using fossil evidence to guide their design and a combination of 3D printed elements and polymers to mimic the flexible columnar structure of the moving appendage, the team demonstrated that pleurocystitids were likely able to move over the sea bottom by means of a muscular stem that pushed the animal forward. Despite the absence of a current day analogue (echinoderms have since evolved to include modern day starfish and sea urchins), pleurocystitids have been of interest to paleontologists due to their pivotal role in echinoderm evolution.

The team determined that wide sweeping movements were likely the most effective motion and that increasing the length of the stem significantly increased the animals' speed without forcing it to exert more energy.

"Researchers in the bio-inspired robotics community need to pick and choose important features worth adopting from organisms," explained Richard Desatnik, PhD candidate and co-first author.

"Essentially, we have to decide on good locomotion strategies to get our robots moving. For example, would a starfish robot really need to use 5 limbs for locomotion or can we find a better strategy?" added Zach Patterson, CMU alumnus and co-first author.

Now that the team has demonstrated that they can use Softbotics to engineer extinct organisms, they hope to explore other animals, like the first organism that could travel from sea to land -- something that can't be studied in the same way using conventional robot hardware.

"Bringing a new life to something that existed nearly 500 million years ago is exciting in and of itself, but what really excites us about this breakthrough is how much we will be able to learn from it," said Phil LeDuc, co-author, and Professor of Mechanical Engineering at Carnegie Mellon University. "We aren't just looking at fossils in the ground, we are trying to better understand life through working with amazing paleontologists."

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How fish survive the extreme pressures of life in the oceans

Scientists have discovered how a chemical in the cells of marine organisms enables them to survive the high pressures found in the deep oceans.

The deeper sea creatures live, the more inhospitable and extreme the environment they must cope with. In one of the deepest points in the Pacific -- the Mariana Trench, 11 kilometers below the sea surface -- the pressure is 1.1 kbar or eight tons per square inch. That is a 1,100-fold increase of the pressure experienced at the Earth's surface.

Under normal or atmospheric pressure, water molecules form a tetrahedron-like network.

Network of water molecules changes shape

At high pressure, though, the network of water molecules begins to distort and change shape. When this happens to the water inside living cells, it prevents vital bio-chemical processes from taking place -- and kills the organism.

In reporting their findings, the researchers in Leeds have for the first time been able to provide an explanation of how a molecule found in the cells of marine organisms counteracts the effect of external pressure on the water molecules.

Professor Lorna Dougan, from the School of Physics and Astronomy at Leeds, said: "Life has adapted to survive and thrive in environmental extremes. In the depths of the oceans, organisms live under extreme high pressures that would destroy human life.

"These high pressures distort the liquid water that resides in all life, resulting in detrimental impacts to the biomolecules that underpin all biological processes.

"We need to understand what happens to water under pressure and how pressure-adapted organisms combat these effects. If we can understand how these organisms survive at extreme pressure, we can apply these findings to the wider study of biomolecular stability."

Trimethylamine N-oxide or TMAO

The molecule found in cells that produces the protective effect against high external pressure is called TMAO -- trimethylamine N-oxide. Studies have shown that the amount of TMAO in ocean-dwelling organisms increases in line with the depth of their habitat.

Led by Dr Harrison Laurent, also from the School of Physics and Astronomy, the study used one of the most advanced analytical facilities in the world to investigate how intense pressure alters the hydrogen bonds between neighbouring water molecules.

Neutron scattering

Called the ISIS Neutron and Muon Source, the analytical facility at the STFC Rutherford Appleton Laboratory in Oxfordshire was used to fire a beam of neutrons -- which are sub-atomic particles -- at samples of water with and without TMAO. The analysis was done at low pressure, 25 bar, and at high pressure, 4 kbar.

The test revealed details of the atomic structure of the water molecules.

At high pressure, the hydrogen bonds in the pure water sample became distorted and less stable and the overall network of water molecules became compacted.

The presence of TMAO, however, strengthened and stabilised the hydrogen bonding and maintained the network structure of the water molecules.

Dr Laurent said: "The TMAO provides a structural anchor which results in the water being able to resist the extreme pressure it is under. The findings are important because they help scientists understand the processes by which organisms have adapted to survive the extreme conditions found in the oceans."

From the study, the research team have also been able to develop what is called an "osmolyte protection ratio," which predicts the level of TMAO needed in the cells of marine organisms so they can survive at a specific depth in the oceans.

Professor Dougan added: "Professor Dougan added: "Our study provides a bridge between water under pressure at the molecular level and the wonderful ability of organisms which thrive under high pressure in depths of the oceans.

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Meltwater influences ecosystems in the Arctic Ocean

In the summer months, sea ice from the Arctic drifts through Fram Strait into the Atlantic. Thanks to meltwater, a stable layer forms around the drifting ice atop the salty seawater, producing significant effects on biological processes and marine organisms. In turn, this has an effect on when carbon from the atmosphere is absorbed and stored, as a team of researchers led by the Alfred Wegener Institute has now determined with the aid of the FRAM ocean observation system. Their findings have just been published in the journal Nature Communications.

Oceans are one of the largest carbon sinks on our planet, due in part to the biological carbon pump: just below the water's surface, microorganisms like algae and phytoplankton absorb carbon dioxide from the atmosphere through photosynthesis. When these microorganisms sink to the ocean floor, the carbon they contain can remain intact for several thousand years. As experts from the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) have now discovered, the meltwater from sea-ice floes can delay this process by four months.

From the summer of 2016 to the summer of 2018, the FRAM (Frontiers in Arctic Marine Monitoring) ocean observation system continually gathered data in Fram Strait (between Greenland and Svalbard). Dense clusters of moorings were installed at two sites in the strait in order to monitor as many aspects of the coupled physical-biological processes in the water as possible. Physical, biogeochemical and acoustic sensors throughout the water column and on the ocean floor, as well as devices that gathered water and sediment samples for subsequent laboratory analysis, were used. "For the first time, for two entire years we were able to comprehensively monitor not only the seasonal developments of microalgae and phytoplankton, but also the complete physical, chemical and biological system in which these developments take place," says Dr Wilken-Jon von Appen, a climate researcher at the AWI and first author of the study.

During this period, the sea-ice export reached two extremes: in the summer of 2017, an extraordinarily large amount of ice was transported out of the Arctic through Fram Strait. This produced a great deal of low-saline meltwater and a pronounced stratification of the water. In contrast, uncharacteristically little ice was transported out of the Arctic in the summer of 2018, which meant there was very little meltwater and therefore no pronounced, salinity-based stratification. The processes involved in the biological carbon pump progressed so differently during these two extremes that the experts refer to them as two different regimes: the meltwater regime (summer of 2017) and the mixed-layer regime (summer of 2018).

Meltwater regime in the summer of 2017

The first algal and phytoplankton blooms appeared on 15 May, when the atmosphere began warming the ocean. In the summer of 2017 a great deal of ice drifted through Fram Strait, producing large quantities of meltwater. "This low-saline water lay atop the saltwater without mixing," says von Appen. "And the stratification between 0 and 30 metres was ten times as intense as between 30 and 55 metres." Consequently, very few nutrients made their way upwards from the deeper water layers, while very little carbon made its way to the seafloor. Phytoplankton growth, which is the first step in the biological carbon pump, took place almost exclusively in the top 30 metres. This intense stratification only collapsed in mid-August, when the atmosphere no longer warmed the water's surface. The majority of the biomass drifted down from the upper layer between September and November, was more than three months old, and was too lacking in nutrients to interest fauna at the ocean floor. In the meltwater regime, during the bloom the microorganisms were able to fix up to 25 grams of carbon per square metre.

Mixed-layer regime in the summer of 2018

The spring and summer of 2018 were another story entirely: conditions were relatively ice-free, which meant less meltwater and less intense stratification of the seawater. A mixed layer formed to a depth of ca. 50 metres. With the first of May came the first diatom blooms; at the same time, the numbers of zooplankton, and of the fish that primarily feed on them, began to rise. Thanks to their faeces, only two to three weeks after the start of the bloom, organic carbon reached depths of up to 1200 metres. Four to seven weeks after the start of the bloom -- almost four months earlier than in the summer of 2017 -- the biomass reached the seafloor. This material was rich in nutrients, attracting five times more fish and benthic fauna than in the meltwater summer. During the bloom, the algae were able to fix roughly 50 grams of carbon per square metre, twice as much as in the meltwater regime.

Despite all these differences between the two regimes, the biological carbon pump wasn't necessarily more productive in the summer of 2018: "We found that, in the summer of 2017, the majority of the organic carbon didn't reach the seafloor until after September," says von Appen. "If you look at the period between early May and late November, the carbon export in the mixed-layer regime was only a third higher than in the meltwater regime." Rather, the pronounced stratification in 2017 promoted longer-term growth over several months, since carbon and nutrients were trapped in the upper layers. In contrast, the ice-free situation in 2018 produced a brief, intense bloom and rapid export, providing food and carbon for deep-sea ecosystems on the ocean floor. As such, the latter would seem to particularly benefit from the summertime conditions in the mixed-layer regime; in the meltwater regime, the intense stratification blocks nutrient input in the summer and deep water mixing in the winter.

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Transforming marine biodiversity discovery and monitoring

A new system for sampling fragments of DNA from marine organisms drifting in the ocean is set to create new opportunities for research on biodiversity and ways of supporting conservation activities.

Over the past decade biodiversity researchers have increasingly used DNA sequences extracted from environmental samples such as soil, marine and fresh water, and even air -- termed environmental DNA (eDNA) -- to identify the organisms present in a huge range of habitats.

Sequencing these tiny traces of DNA has proved to be a powerful technique for detecting elusive species that may only rarely be observed directly, or in early life stage, when they may be difficult to identify, revolutionising biodiversity discovery and monitoring.

Researchers from the University of Leeds and University of Milano-Bicocca in Italy have developed an innovative new approach for collecting marine eDNA samples which promises to open up biodiversity monitoring of remote offshore ocean locations.

The team has developed a novel system for easy sampling that can be deployed from ocean-going ferries and other commercial vessels such as container ships, allowing the possibility of using the global commercial shipping fleet to help monitor marine biodiversity.

Although DNA sequencing is becoming more cost-effective every year, the biggest challenge is often collecting samples over the large geographic areas needed to scale up these new monitoring techniques to a global reach.

Sampling marine eDNA far from land usually depends on access to dedicated research vessels, which are complex and expensive to operate. These logistical constraints limit the geographic scope and frequency of surveys, impeding the expansion of large scale eDNA surveys.

The new system does not require complex equipment deployed from a ship; water is collected from the engine cooling system with simple apparatus and can be carried out by non-specialists. Since commercial vessels regularly cross remote corners of most of the world's oceans, they could provide almost limitless opportunities for sample collection to contribute to biodiversity monitoring programmes.

The team collaborated with the company Corsica-Sardinia Ferries, which supports a long-term visual survey programme for cetaceans run by ISPRA (Italian Institute for Environmental Protection and Research; also a partner in the current study), to test the system, on their route between Livorno in Tuscany, and Golfo Aranci in Sardinia.

The results showed the ferry-collected samples had traces of DNA from all parts of the vertebrate ecosystem, ranging from small prey fish at the base of the food chain, such as anchovies and sardines, through small and larger predatory fish such as tuna and swordfish, all the way to dolphins, and ocean giants including fin and sperm whales.

Co-lead author Dr Simon Goodman, from the School of Biology, University of Leeds, is co-lead author of the report, published in Frontiers in Marine Science.

He said: "When we first started to dig into the sequencing results I was astounded as to how well it had captured the structure of the vertebrate ecosystem.

"It's a really exciting result and highlights the power that eDNA has for revealing fine scale ecological variation."

One of the study leads, Dr Elena Valsecchi from the Department of Environmental and Earth Sciences, the University of Milano-Bicocca, said: "This innovative methodology applied to environmental DNA allows us to make a sort of CAT (computerized axial tomography) scan of the sea.

"Next we will be scanning multiple ferry routes in the Mediterranean in order to produce a high-resolution "image" on the state of biodiversity in our seas."

Overall eDNA from 100 unique vertebrate species were detected, with species composition proving to be a good match for that known from the Mediterranean from conventional survey techniques.

In addition, the team detected fine scale variation in species occurrence related to environmental factors, such as that the relative abundance of sequences for anchovy and sardines correlated with the different water temperatures the species are known to prefer for spawning.

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