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Something peculiar is happening in the azure waters off the rocky cliffs of Ischia, Italy. There, streams of gas-filled volcanic bubbles rising up to the surface are radically changing life around them by making seawater acidic. Stanford researchers studying species living near these gassy vents have learned what it takes to survive in acidic waters, providing a glimpse of what future oceans might look like as they grow more acidic.

Volcanic carbon dioxide seeps from the ocean floor near Ischia, Italy [Credit: Pasquale Vassallo, Stazione Zoologica Anton Dohrn]

Their findings, published in Nature Communications, suggest that ocean acidification driven by human-caused carbon dioxide emissions could have a larger impact than previously thought.

"When an organism's environment becomes more acidic, it can dramatically impact not only that species, but the overall ecosystem's resilience, function and stability," said Stanford marine biologist Fiorenza Micheli, lead author on the paper. "These transformations ultimately impact people, especially our food chains."

A natural laboratory

Most ocean acidification studies to date have taken place in laboratories, making it impossible to assess how whole ecosystems comprised of multiple, interacting species would be affected. The real-life laboratory provided researchers an opportunity to examine dozens of species, from sea urchins to marine snails, that live in areas of different acidity along Ischia's volcanic carbon dioxide vents. In addition to studying how species diversity changed with acidification, they analyzed species traits, such as diet and growth, that influence how well the ecosystem performs. For example, sea snails were smaller in more acidic water, as their shells take longer to grow and are thinner and more brittle. These harmful effects on sea snails, a key food for animals higher up in the food chain, may affect fish populations.

Overall, the researchers found that the active venting zones with the most acidic waters were home to not only the least number of species, but also the lowest amounts of "functional diversity" – the range of ecosystem-support services or roles that each species can provide.

"Studying the natural carbon dioxide vents in Ischia allowed us to unravel which traits from different species, like snail shell strength, were more vulnerable to ocean acidification. These results illuminate how oceans will function under different acidification scenarios in the future," said lead author Nuria Teixidó, a marine biologist from Stazione Zoologica Anton Dohrn in Italy, who was a visiting researcher at Stanford during the research.

Acidification in the waters of Ischia displaced long-lived species, such as corals, that form habitat for other species – a process already often witnessed on reefs across the world. The researchers also found that high levels of carbon dioxide and more acidity favored species with short life spans and fast turnover as they are the only species that can resist these environmental conditions. This change could lead to further diversity loss and instability in the oceans, as biodiversity tends to increase an ecosystem's stability.

Biodiversity loss is mapped along a natural CO2 gradient [Credit: Nuria Teixidó, Stazione Zoologica Anton Dohrn]

A broader application

Localized case studies such as Ischia can shed light on how future global environmental conditions may affect ocean life. Beyond losing biodiversity, ocean acidification will threaten food security for millions of people who depend on seafood, along with tourism and other ocean-related economies.

"The effects of ocean acidification on whole ecosystems and their functioning are still poorly understood," said Micheli, a professor of biology. "In Ischia, we have gained new insights into what future oceans will look like and what key services, like food production and coastal production, will be lost when there is more carbon dioxide in the water."

Author: Nicole Kravec | Source: Stanford University [December 11, 2018]

Barely living "zombie" bacteria and other forms of life constitute an immense amount of carbon deep within Earth's subsurface -- 245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth's innermost secrets.

A nematode (eukaryote) in a biofilm of microorganisms. This unidentified nematode (Poikilolaimus sp.) from Kopanang gold mine in South Africa, lives 1.4 km below the surface [Credit: Gaetan Borgonie, Extreme Life Isyensya, Belgium]

On the eve of the American Geophysical Union's annual meeting, scientists with the Deep Carbon Observatory today reported several transformational discoveries, including how much and what kinds of life exist in the deep subsurface under the greatest extremes of pressure, temperature, and low nutrient availability.

Drilling 2.5 kilometers into the seafloor, and sampling microbes from continental mines and boreholes more than 5 km deep, scientists have used the results to construct models of the ecosystem deep within the planet.

With insights from now hundreds of sites under the continents and seas, they have approximated the size of the deep biosphere -- 2 to 2.3 billion cubic km (almost twice the volume of all oceans) -- as well as the carbon mass of deep life: 15 to 23 billion tonnes (an average of at least 7.5 tonnes of carbon per cu km subsurface).

The work also helps determine types of extraterrestrial environments that could support life.

Among many key discoveries and insights:

- The deep biosphere constitutes a world that can be viewed as a sort of "subterranean Galapagos" and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)

- Two types of microbes -- bacteria and archaea -- dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial "dark matter" dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth's bacteria and archaea live in the subsurface

- Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks

- The genetic diversity of life below the surface is comparable to or exceeds that above the surface

- While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous -- they appear planet-wide

- Microbial community richness relates to the age of marine sediments where cells are found -- suggesting that in older sediments, food energy has declined over time, reducing the microbial community

- The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth's hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth's surface, in an uninhabited Iranian desert, is about 71°C -- the temperature of well-done steak)

- The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level

- Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

Candidatus Desulforudis audaxviator (the purplish, blue rod-shaped cells straddling orange carbon spheres) is a species of bacteria that survives on hydrogen. Scientists found it living within a fluid and gas-filled fracture 2.8 km beneath Earth's surface at a mine near Johannesburg, South Africa. The genus name Desulforudis comes from the Latin for "from sulfur"  and "rod," noting its shape and its ability to get energy from sulfates. And audaxviator? From Jules Verne's Journey to the Center of the Earth, and a message in Latin deciphered by Verne's protagonist, Professor Lidenbrock, which read  in part: "descend, bold traveler, and attain the center of the Earth" [Credit: Greg Wanger, California Institute of Technology, USA, and Gordon Southam University of Queensland, Australia]

Ever-increasing accuracy and the declining cost of DNA sequencing, coupled with breakthroughs in deep ocean drilling technologies (pioneered on the Japanese scientific vessel Chikyu, designed to ultimately drill far beneath the seabed in some of the planet's most seismically-active regions) made it possible for researchers to take their first detailed look at the composition of the deep biosphere.

There are comparable efforts to drill ever deeper beneath continental environments, using sampling devices that maintain pressure to preserve microbial life (none thought to pose any threat or benefit to human health).

To estimate the total mass of Earth's subcontinental deep life, for example, scientists compiled data on cell concentration and microbial diversity from locations around the globe.

Led by Cara Magnabosco of the Flatiron Institute Center for Computational Biology, New York, and an international team of researchers, subsurface scientists factored in a suite of considerations, including global heat flow, surface temperature, depth and lithology -- the physical characteristics of rocks in each location -- to estimate that the continental subsurface hosts 2 to 6 × 10^29 cells.

Combined with estimates of subsurface life under the oceans, total global Deep Earth biomass is approximately 15 to 23 petagrams (15 to 23 billion tonnes) of carbon.

Says Mitch Sogin of the Marine Biological Laboratory Woods Hole, USA, co-chair of DCO's Deep Life community of more than 300 researchers in 34 countries: "Exploring the deep subsurface is akin to exploring the Amazon rainforest. There is life everywhere, and everywhere there's an awe-inspiring abundance of unexpected and unusual organisms.

"Molecular studies raise the likelihood that microbial dark matter is much more diverse than what we currently know it to be, and the deepest branching lineages challenge the three-domain concept introduced by Carl Woese in 1977. Perhaps we are approaching a nexus where the earliest possible branching patterns might be accessible through deep life investigation.

"Ten years ago, we knew far less about the physiologies of the bacteria and microbes that dominate the subsurface biosphere," says Karen Lloyd, University of Tennessee at Knoxville, USA. "Today, we know that, in many places, they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live.

"Today too, we know that subsurface life is common. Ten years ago, we had sampled only a few sites - the kinds of places we'd expect to find life. Now, thanks to ultra-deep sampling, we know we can find them pretty much everywhere, albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere."

"Our studies of deep biosphere microbes have produced much new knowledge, but also a realization and far greater appreciation of how much we have yet to learn about subsurface life," says Rick Colwell, Oregon State University, USA. "For example, scientists do not yet know all the ways in which deep subsurface life affects surface life and vice versa. And, for now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth."

"A decade ago, we had no idea that the rocks beneath our feet could be so vastly inhabited. Experimental investigations told us that microbes could potentially survive to great depth; at that time, we had no evidence, and this has become real ten years later. This is simply fascinating and will surely foster enthusiasm to look for the biotic-abiotic fringe on Earth and elsewhere," said Isabelle Daniel, University of Lyon 1, France.

This is a species of Methanobacterium, which produces methane. Found in samples from a buried coal bed 2 km below the  Pacific Ocean floor off the coast of Japan, this specimen was retrieved during an Integrated Ocean Drilling Program  (now the International Ocean Discovery Program) expedition aboard the Drilling Vessel Chikyu. Bar represents 10 μm (micrometers, or 0.0004 inch) [Credit: Hiroyuki Imachi (Japan Agency for Marine-Earth Science and Technology (JAMSTEC)]

Among the many remaining enigmas of deep life on Earth:

Movement: How does deep life spread -- laterally through cracks in rocks? Up, down? How can deep life be so similar in South Africa and Seattle, Washington? Did they have similar origins and were separated by plate tectonics, for example? Or do the communities themselves move? What roles do big geological events (such as plate tectonics, earthquakes; creation of large igneous provinces; meteoritic bombardments) play in deep life movements?

Origins: Did life start deep in Earth (either within the crust, near hydrothermal vents, or in subduction zones) then migrate up, toward the sun? Or did life start in a warm little surface pond and migrate down? How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?

Energy: Is methane, hydrogen, or natural radiation (from uranium and other elements) the most important energy source for deep life? Which sources of deep energy are most important in different settings? How do the absence of nutrients, and extreme temperatures and pressure, impact microbial distribution and diversity in the subsurface?

"Even in dark and energetically challenging conditions, intraterrestrial ecosystems have uniquely evolved and persisted over millions of years. Expanding our knowledge of deep life will inspire new insights into planetary habitability, leading us to understand why life emerged on our planet and whether life persists in the Martian subsurface and other celestial bodies,"  according to Fumio Inagaki, Japan Agency for Marine-Earth Science and Technology.

"While we are far from being able to quantify it, we believe Deep Life has an important impact on global biogeochemical cycles and chemical equilibria in habitable rocks. Deep Life plays a role in aquifer quality, for example, or carbon capture and storage (CCS). Unfortunately, the deep biosphere is very poorly considered in engineering operations carried out in the subsurface. We recently demonstrated the high reactivity of deep biota to CO2 injections (CCS), which ultimately led to the bioclogging of the injection well, and surrounding reservoir," adds Benedicte Menez, Institut de Physique du Globe de Paris, France.

Source: Deep Carbon Observatory [December 10, 2018]

The future of the world's coral reefs is uncertain, as the impact of global heating continues to escalate. However, according to a study published in Nature Climate Change, the response of the Great Barrier Reef to extreme temperatures in 2017 was markedly different to one year earlier, following two back-to-back bouts of coral bleaching. Remarkably, corals that bleached and survived 2016 were more resistant in 2017 to a recurrence of hot conditions.

Researchers found that the response of corals to heat stress during the second of two unprecedented back-to-back bleaching events on the Great Barrier Reef was markedly different from the first [Credit: Tane Sinclair-Taylor]

"Dead corals don't bleach for a second time. The north lost millions of heat-sensitive corals in 2016, and most of the survivors were the tougher species. As a result of bleaching, the mix of species is changing very rapidly," said lead author Prof Terry Hughes, Director of the Australian Research Council Centre of Excellence for Coral Reef Studies (Coral CoE), headquartered at James Cook University.

"We were astonished to find less bleaching in 2017, because the temperatures were even more extreme than the year before," he said.

The new research highlights the extent of damage, or "geographic footprint" of multiple coral bleaching events across the 2,300 km length of the world-heritage listed area.

The back-to-back heatwaves bring the total number of mass bleaching events on the Great Barrier Reef to four over the past two decades (in 1998, 2002, 2016 and 2017). The scientists found that only 7% of the Great Barrier Reef escaped bleaching entirely since 1998, and after the 2017 event, 61% of reefs have now been severely bleached at least once.

During an underwater survey, a researcher records the bleaching severity of a massive Porites coral colony on the Great Barrier Reef [Credit: Justin Marshall]

"We found, using the National Oceanic and Atmospheric Administration's (NOAA) satellite-based coral bleaching tools, that corals in the north of the Great Barrier Reef were exposed to the most heat stress in 2016. A year later, the central region saw the most prolonged heating," said co-author Dr Mark Eakin, from NOAA's Coral Reef Watch program, in Maryland, USA.

The southern third of the Great Barrier Reef was cooler in both years due to local weather conditions, and escaped with only minor bleaching.

"It's only a matter of time before we see another mass-bleaching event, triggered by the next marine heatwave, driven by global heating," said co-author Dr Andrew Hoey of Coral CoE at James Cook University. "One of the worst possible scenarios is we'll see these southern corals succumb to bleaching in the near future."

"The outcome in 2017 depended on the conditions experienced by the corals one year earlier. We called that 'ecological memory,' and show that these repeating events are now acting together in ways that we didn't expect," said Prof Hughes.

"We've never seen back-to-back mass coral bleaching before on the Great Barrier Reef, in two consecutive summers. The combined footprint has killed close to half of the corals on two-thirds of the world's largest reef system," said Dr Hoey.

"We need urgent global action on greenhouse emissions to save the world's coral reefs. Australia should be -- but regrettably isn't -- at the forefront of tackling global heating," said Prof Hughes.

Source: ARC Centre of Excellence in Coral Reef Studies [December 10, 2018]

A UMass Boston professor and his colleagues have published new research showing that feeding on human junk food may be altering the course of evolution in Darwin's finches.

Finches eat off a plate in an urban area of the Galapagos [Credit: K. Gotanda]

Assistant Professor of Evolutionary Biology Luis De León says feeding on human foods is weakening natural selection on ground finch beaks, which is what drives the formation of new species in the wild. These findings, published in the journal Evolutionary Applications, suggest that the seemingly harmless activity of feeding birds might be altering the course of evolution in the iconic Darwin’s finches in the Galápagos islands.

“If we continue to feed finches, we’re not only affecting the individual species, but the processes that lead to the formation of new species,” De León said. “We’re getting in the way of evolution.”

Galápagos finches are famed for being the inspiration behind Charles Darwin’s pioneering work on evolution. They are an example of adaptive radiation, an evolutionary process that produces new species from a single, rapidly diversifying lineage. Their common ancestor arrived on the Galápagos about two million years ago, and since then Darwin's finches have evolved into more than a dozen recognized species differing in body size, beak shape, and feeding behavior.

De León and fellow researchers from UMass Amherst, Universidad San Francisco de Quito, McGill University, and Norwegian University of Science and Technology were on Santa Cruz Island when they found two forms of medium ground finches — a small and large version — while studying beak size at an isolated, pristine site.

When they repeated the same set of measurements at a nearby urban site, the distinction between the two beak sizes was not present. Studying data collected by other researchers in the 1970s, the researchers could see the two types of medium ground finches had been present in the area before, but something had changed in the last 40-50 years.

They hypothesized that the change might have to do with urbanization and the rapidly increasing human population in that area. In particular, the introduction of novel foods brought by humans.

Finches eat from an egg crate left by the researchers [Credit: University of Massachusetts Boston]

Using egg crates filled with natural seeds and human junk food — chips, cookies, and rice — the researchers tested to see if the finches were in fact feeding on human food and what their preference was, weighing the food before and after to see how much was eaten.

De León said they found that finches in the urban area were almost exclusively feeding on human food. When the experiment was repeated at an isolated site in nature, the finches ignored the trays.

They found that "urban" finches feed on human junk foods, and in fact prefer these foods over their natural diet. This indicates that ongoing urbanization in the Galápagos is eroding the ecological differences that originally drove the formation of species in Darwin's finches.

“In contrast to their natural diet, the finches are changing their diet to human junk food,” De León said. “We know one way finches diversify and become new species is by specializing in different food types. All three or four species of ground finches at urban sites on Santa Cruz Island seem to be converging onto the same junk food diet. If that’s the case, the selection pressures that would be naturally  keeping them apart would be weakening, possibly leading to the collapse of the adaptive radiation of ground finches.”

Researchers also found a strong preference for human foods at EG Beach, a non-urban site visited by tourists located 12 kilometers away from the town of Puerto Ayora. This suggests that human behavior, rather than human population density, is the main driver of finches’ preference for human food, expanding the impacts of urbanization beyond city centers.

Now that the researchers know that finches are changing their diets to human junk food, they need to look at the consequences for the actual evolution of the species on this island.

“When thinking about preserving biodiversity in general, we often focus on preserving individual species,” he said. “What we show with this work is we also need to consider preserving the processes that lead to the formation of species.”

Assistant Professor of Evolutionary Biology Luis De León studies Darwin's finches [Credit: University of Massachusetts Boston]

De León and a PhD student will return to the Galapagos in January.

De León said they will continue to do more genetic analysis, looking at whether there is an increase in gene flow across the four species of ground finch. Now that the birds are eating the same diet, researchers want to know if they are also interbreeding.

Elaine Montes, a second-year PhD student at UMass Boston who is working with De León, will look at the physiological consequences of human junk food on Galapagos finches by analyzing telomeres, a long chain of repetitive DNA at the end of every chromosome that can shorten due to stress and aging.

“We want to see whether they have a shorter life span than birds in nature,” he said.

De León has worked at UMass Boston for two years. He received his PhD at McGill University, where he started his work on Galapagos finches 14 years ago.

“It’s a fascinating place. Every species is so unique; it captures your imagination. You can imagine how Darwin was fascinated by looking at all those species,” he said. “I feel privileged to essentially walk in Darwin’s footsteps.”

Author: Crystal Valencia | Source: University of Massachusetts Boston [December 03, 2018]