Tag Archives: ecosystem

Different cities have their own microbial fingerprint, a global study reports

An international team of researchers says that every city has its own fingerprint — in the shape of pathogens.

Image credits Denis Poltoradnev.

The largest ever genetic study of urban microbiomes (including both surfaces and the air in 60 cities worldwide) reports that each city has its own microbial fingerprint. The project sequenced and analyzed samples from public transit systems and hospitals in cities around the world, identifying thousands of viruses, bacteria, and two archaea not found in reference databases.

Roughly 4,730 different samples, taken from cities on six continents over the course of three years were used as part of this study, the team explains. The analysis also revealed a set of 31 species that were found in 97% of the samples.


“Every city has its own ‘molecular echo’ of the microbes that define it,” says senior author Christopher Mason, a professor at Weill Cornell Medicine (WCM) and the director of the WorldQuant Initiative for Quantitative Prediction.

“If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came.”

This study is the first systematic, worldwide catalog of urban microbial ecosystems, according to the authors. Despite the breadth of the results here, the team is confident that any subsequent sampling of this kind will continue to find new species.

The paper draws its roots in 2013, when Mason started collecting and analyzing microbial samples in the New York City subway system. After publishing his findings, Mason was contacted by other researchers from around the world who wanted to perform similar analyses in their own cities. So he worked out a protocol that they could follow, posting it on YouTube. Samples were to be collected using DNA- and RNA-free swabs and sent to a lab at WCM for analysis along with controls. Most of the analysis part was handled by an Extreme Science and Engineering Discovery Environment (XSEDE) supercomputer in Pittsburgh.

Two years later, in 2015, Mason created the International MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) Consortium to better handle all the data people were sending him. Samples from air, water, and sewage were now coming in from across the world in addition to those from hard surfaces.

Such genomic studies can help detect outbreaks of both known and unknown infections and can help us keep tabs on the levels of antibiotic-resistant microbes in different urban environments. It’s also a very useful tool when analyzing the evolution of microbial life.

“There are millions of species on Earth, but we have a complete, solid genome reference for only 100,000 to 200,000 at this point,” Mason says, explaining that the discovery of new species can help with the building of microbial family trees to see how different species are related to one another.

“Based on the sequence data that we’ve collected so far, we’ve already found more than 800,000 new CRISPR arrays,” he says. Additionally, the findings indicate the presence of new antibiotics and small molecules annotated from biosynthetic gene clusters (BGCs) that have promise for drug development.

These samples led to the results published in this paper: 4,246 known species of microorganisms were identified worldwide, 31 of which were present in 97% of all samples from urban areas.

“One of the next steps is to synthesize and validate some of these molecules and predicted  biosynthetic gene clusters (BGCs), and then see what they do medically or therapeutically,” Mason says. “People often think a rainforest is a bounty of biodiversity and new molecules for therapies, but the same is true of a subway railing or bench.”

The paper “”A global metagenomic map of urban microbiomes and antimicrobial resistance” has been published in the journal Cell.

The world’s largest ecosystems could collapse in decades — much faster than previously thought

The Amazon rainforest ecosystem could collapse in as little as 49 years and the Caribbean coral reefs in only 15 years, a new study warns which found large ecosystems are more vulnerable than previously thought.

Photo from within the Amazon Rainforest in Tena, Ecuador. Credit: Jay, Flickr.

By now, it should come as no surprise that human activity is applying intense pressure on the planet’s natural systems, threatening thousands of species with extinction.

At sea, a third of marine mammals, reef-forming corals, sharks, and shark relatives are on the brink of extinction. Life on land isn’t faring any better. Humans have significantly altered three-quarters of the earth’s land surface area, leaving more than half a million species without enough habitat to survive. 

This is dangerous since some ecosystems can simply collapse once it has lost its defining environmental or natural features or if they are replaced by a different type of ecosystem. Clear lakes can turn green, coral reefs can get bleached, and forests can turn into savanna grasslands following massive deforestation.

Researchers at the University of Southampton, England, and the University of Bangor, Wales, analyzed the transformations incurred by 40 natural environments on land and in waters. Their size varied from small ponds to marine ecosystems.

The findings suggest that large ecosystems take longer to collapse than smaller ones, owing to their sheer size. However, the rate at which large ecosystems become vulnerable to collapse is significantly faster than the rate of change of smaller systems.

Writing in the journal Nature Communications, the authors claim that these findings can be explained by the fact that larger natural systems are made up of multiple sub-systems of species and habitats.

These ecological compartments provide resilience against stress in the initial phase of the transformation. However, once a certain threshold is crossed, the same modularity contributes to an acceleration of the system’s collapse.

“The challenging part was to manipulate a series of models to see if they showed the same relationships.  It required many months of simulations often using a super-computer but overall the model simulations support the observed findings. The ‘Aha’ moment was when we realised the relationship was sub-linear meaning the speed of collapse per unit area increases as the total area increases,” John Dearing, Professor in Physical Geography at the University of Southampton, told ZME Science.

“Large systems will take longer to tip from one state to another – because the stresses take longer to spread across larger distances.  But the rate of tipping is relatively more quickly in large systems so a forest that’s a hundred times bigger than another forest will take much less than a hundred times the time to collapse,” he added.

In fact, the researchers found that huge ecosystems that have existed for thousands of years could collapse in as little as 50 years.

“We worked in China trying to understand why lakes had quickly shifted from clear water to ‘green’ water with algal blooms. We simply asked the question about how the size of a lake would affect how quickly it shifted into the ‘green’ state – and started to collect published data where this had already been observed,” Dearing said.

According to the researchers, the main threats for forest ecosystems are deforestation and disease; nutrients from the catchment and poor fish management for lakes; silt and over-fishing for coral reefs — ” and all of these interact with global warming to make ecosystems less resilient and therefore more vulnerable,” Dearing added.

A prime example of the unraveling effects presented in the new study is represented by the recent bushfires in Australia — the worst in recorded history.

In the future, Dearing and colleagues plan on conducting more modeling to gain even more insight into how ecosystem collapse unfolds.

“The public should be worried.  It means that large, iconic ecosystems like the Amazon forest could collapse much more quickly than we might intuitively expect.  Once deforestation and global warming stress the forest to the point that it reaches a tipping point, it could be a matter of a few decades before the whole forest shifts into a grassland,” Dearing concluded.

“It’s yet another warning about the potentially irreversible damage that’s being done to global ecosystems –  damage that threatens biodiversity, the food and other ecosystem services that we depend upon, the wellbeing of local communities, and the stability of other interdependent systems, like regional climate  – and all happening much more quickly than we might think.”

Ecosystems with varied plant species are lusher, more efficient

Greater plant diversity benefits everyone in the ecosystem, a new study reports.

Image credits Tien Vu.

Higher levels of plant diversity allow ecosystems to utilize more energy and more efficiently, new research found. Ecosystems with 60 or more plant species contained twice the amount of living biomass, on average, than ecosystems built on plant monocultures.

This is the first study to look at energy flow throughout an entire ecosystem; previous efforts of this type only focused on a single feeding type (or ‘trophic level’), such as herbivore or carnivore.

Trickle-up energonomics

“We have analyzed an entire feeding network — in other words, multitrophic interactions — above- and belowground. This is indispensable for understanding the effects resulting from global species extinction,” explained Dr. Sebastian T. Meyer, a researcher at the Chair for Terrestrial Ecology at the Technical University of Munich (TUM) and lead author of the study.

Aboveground food chains are those that form, you’ll be surprised to hear, above the ground. One such food chain could, for example, start with grasses, extending to grasshoppers, and finally spiders. Belowground food chains are also very important for the health of an ecosystem and include such elements as bacteria, plant roots, and other burrowing species.

What the team analyzed were energy flows inside these food chains and the wider ecosystem. They looked at how much energy flows into the system (this is handled exclusively by plants), how much remains in the system, i.e. how much biomass is present, and how much energy is leaving the system. They used data gathered through the Jena Experiment a large-scale biodiversity mapping program first started in 2002.

The team established the trophic networks that form in each of the 80 plots of the Jena Experiment, the standing biomass at each level, and how energy flows through the networks. All in all, the ecosystems with the most plant biodiversity showed more efficient use of energy.

“The study shows that higher plant diversity leads to more energy stored, greater energy flow and higher energy-use efficiency in the entire trophic network, therefore across all trophic levels,” explained Dr. Oksana Buzhdygan from Freie Universitaet Berlin, co-lead author of the study.

“Seeing positive effects on one level does not imply that there cannot be simultaneous positive effects on other feeding levels,” said Dr. Meyer.

He notes that high plant biodiversity can keep ecosystems stable even when faced with high consumption lower down the food chain. Furthermore, the team explains that higher plant diversity makes ecosystems more resilient in the face of perturbations.

The findings showcase the benefits that may be obtained from increasing plant diversity in various ecosystems, from urban parks to croplands. Planting mixed crops, for example, can help maintain healthy ecosystems with virtually no effort on our part.

The paper “Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands” has been published in the journal Nature Ecology & Evolution.

Tropical forests and coral reefs are buckling under interacting threats

Climate change, extreme weather, and human pressure are causing ecosystems across the tropics to collapse, a new study reports.

Image via Stokpic

The authors analyzed over 100 locations where tropical forests and coral reefs have been affected by hurricanes, floods, heatwaves, droughts, fires, and other types of extreme climate. The findings expand our understanding of the health of these ecosystems, especially in the wider context of climate change and damage caused by human activity.

The findings weren’t encouraging. The team echoes previous research and warns that only decreasing CO2 emissions can help reverse the damaging trend of climate change on ecosystems.

Compounding issues

“Tropical forests and coral reefs are very important for global biodiversity, so it is extremely worrying that they are increasingly affected by both climate disturbances and human activities,” says lead researcher Dr. Filipe França from the Embrapa Amazônia Oriental in Brazil and Lancaster University. “Many local threats to tropical forests and coral reefs, such as deforestation, overfishing, and pollution, reduce the diversity and functioning of these ecosystems. This in turn can make them less able to withstand or recover from extreme weather.”

“Our research highlights the extent of the damage which is being done to ecosystems and wildlife in the tropics by these interacting threats.”

Climate change is causing an increase in the frequency and strength of storms and marine heatwaves, which are very damaging to coral reefs; they both reduce the cover of live coral (i.e. they shrink reefs) and cause long-lasting changes in coral and fish communities, which reduce their ability to reduce further impacts.

On land, tropical forests are also threatened by more frequent and extreme hurricanes, the team explains. Such storms cause the destruction of plants which in turn affects the whole of the ecosystem, as animals, birds, and insects directly rely on the plants for food and shelter. The team explains that in some regions, such as the Caribbean, extreme weather events have decimated wildlife by more than half.

Finally, the interplay between higher average temperatures and shifting precipitation patterns has led to a rise in large-scale wildfires in the tropics, the team explains.

“We are starting to see another wave of global extinctions of tropical birds as forest fragmentation reduces populations to critical levels,” explained Dr Alexander Lees, from Manchester Metropolitan University, co-author of the paper.

The team took the 2015 El Niño as an example. One of the areas that felt its impact the most was Santarém, a city in the Brazilian state of Pará, which experienced “a severe drought and extensive forest fires” that affected local wildlife, the team explains. The drought associated with El Niño impaired the forests’ ability to recover from these fires by affecting dung beetles. The species plays a key role in spreading seeds in the forest, and the dry conditions during the 2015-2016 El Niño caused their activity levels to plummet. Coral reefs were also critically damaged by the same El Niño, explains Professor Nick Graham from Lancaster University.

“The 2015-16 coral bleaching event was the worst ever recorded, with many locations globally losing vast tracts of valuable corals,” he explained.

“Worryingly, these global bleaching events are becoming more frequent due to the rise in ocean temperature from global warming.”

The team underlines that we need new conservation strategies to help ecosystems — especially rainforests and coral reefs — handle multiple, concurrent threats and that we need them fast. However, they also explain that local action may simply not be enough if we don’t tackle global climate change.

The paper “Climatic and local stressor interactions threaten tropical forests and coral reefs” has been published in the journal Philosophical Transactions of the Royal Society B: Biological Sciences.

What is biodiversity

A shorthand of the terms ‘biological diversity’, biodiversity refers to the variety of life, in all its forms and all its levels, on Earth. But why do we need biodiversity? Can’t we just have a planet populated solely with humans and those few plants and animals that are tasty?

We probably could, for a few days — then everything would grind to a halt (i.e. everything dies). Let’s see why.

Levels of biodiversity

In general, biodiversity is considered at three (progressively-wider) levels: genetic diversity, species diversity, and ecosystem diversity.

Genetic diversity refers to the level of genetic variety within a single species. While individuals of the same species are very similar from a genetic point of view, there’s also surprising variation between them. Individuals can show genetic differences between one another, as well as whole groups or populations. For example, two sparrows in New York will be a little different, genetically speaking. The differences between a sparrow in London and one in New York, however, would be much more pronounced.

Not all groups have the same degree of genetic diversity. For example, kangaroos come from a relatively recent evolutionary line, and are thus pretty similar from a genetic standpoint. Dasyurids, a group of carnivorous marsupials that includes the Tasmanian Devil, the Numbat, and quolls, come from a more ancient lineage and are far more diverse (as they’ve had more time to develop).

Image via Pixabay.

Species diversity refers to the number of different species that live in a particular area or habitat. Some habitats harbor a lot of species diversity — mountain ranges or coral reefs come to mind. Others, such as salt flats or heavily polluted areas that aren’t very nice places to live in, have very poor diversity.

The world might seem to be bursting at the seams with life, but it’s actually not that diverse a place; unless you count invertebrates. Invertebrates are animals that lack a spine and make up about 99% of all animal species. The group includes crabs, snails, worms, corals, and sea stars, but is overwhelmingly represented by insects. The good news, however, is that insects are surprisingly adaptable and versatile and end up fulfilling many vital ecosystem roles (more on that later).

Ecosystem diversity represents the variety of different ecosystems in a given area. An easy way to think of ecosystems is to imagine them as natural, local ‘economies’ that are affected by factors pertaining to their physical environment (local climate, precipitation levels, soil composition, etc) and the make-up and interaction of the species that live in said environment. An ecosystem is the product of the organisms interacting with the environment.

What has biodiversity ever done for us?

Coral reefs are some of the most biodiverse ecosystems out there.
Image via Pixabay.

You’d literally be dead without it.

One of the things you start to notice when studying biology is that life has a very interesting way of enabling life (the “Gaia hypothesis“). To help you get an idea of what I mean, let’s take a look at early life on Earth.

The first things to ever live around here were simple, microscopic things — bacteria, basically. The first direct evidence of life on Earth hails from around 3.5 billion years ago (fossilized microorganisms found in Apex chert rocks in the Pilbara Craton, Australia), but life likely evolved a bit earlier. It probably wasn’t very easy to make a living on Earth back in the day, however; these organisms likely lived in colonies around hydrothermal vents. These vents put out heat and chemical compounds, which the bacteria could capture to eke out energy from. This type of metabolism, which is known as chemolithoautotrophic (which means “self-feeding on chemicals and rocks), generates very little energy compared to oxygen respiration.

Image credits Schmidt Ocean Institute via USGS.

Humans can exist in the form we have today because, unlike those early bacteria, we have ample access to oxygen to breathe. That oxygen, however, wasn’t always there — bacteria and plants released it into the atmosphere over the course of geological time. In other words, we can exist as we do today because life, over millions and billions of years, worked to create the conditions we live in.

But… that’s just life doing its thing, right? How does biodiversity fit into this story? Well, the short of it is that biodiversity is what keeps life and ecosystems going — life as we know it today requires a baseline of biodiversity to work.

Why biodiversity is the spice of life

Image via Pixabay.

Diversity is life’s insurance policy. As a rule of thumb, the more genetically-diverse a species is, the better its chances of not going extinct; ecosystems with greater species diversity are more resilient to shocks such as invasive species, climate shifts, or meteorites. Areas with greater ecosystem diversity can take more ‘damage’ (lose more ecosystems) before things break down completely. Let’s expand on each of those points independently.

First, consider the banana. Chances are that every banana you’ve even gulped down is, on a genetic level, exactly the same as every other banana you’ve ever eaten. That’s because the banana cultivar you’re overwhelmingly likely to encounter is a Cavendish banana (95% of all commercially-available bananas). All Cavendish bananas are clones of one another. The plants are propagated through the use of suckers, lateral offshoots of a parent plant that are cut and planted in the soil.

The reason Cavendish is so prominent today is that the original (and better-tasting) banana cultivar, the Gros Michel, was virtually wiped clean away from South America by the Panama disease. Why did this fungus-driven disease have such an easy time destroying the Gros Michel? Well, just like the Cavendish, Gros Michel bananas were basically clones of one another — so a pathogen that could infect and kill one plant could infect and kill all its species. The only reason the Gros Michel variety isn’t extinct right now is that some cultures survived in other areas of the world where the Panama disease hasn’t (as of now) reached. This example illustrates why insufficient genetic diversity can spell doom for a species.

Koa e Kea variety of banana afflicted by Fusarium wilt (Panama disease).
Image credits Scot Nelson / Flickr.

To understand why species diversity matters, we have to talk about ecological niches. Just like you have a job (if not, good luck), your neighbor has a job, and so on, each species has a ‘job’ it performs for the ecosystem. We call these jobs ‘ecological niches’. If the job doesn’t get done, the whole thing starts to crack. If enough jobs don’t get done, the local economy (ecosystem) collapses completely.

Let’s take pollinators as an example. They zip this way and that carrying pollen, thus fertilizing plants and crops, and indirectly helping to grow things for everyone to eat. If a single species is performing this role, and it gets wiped out for some reason, a critical ecosystem ‘service’ or ‘function’ (pollination) won’t be performed. Some, like plants, act as suppliers of food; herbivores harvest and concentrate nutrients and energy from plants, and carnivores keep herbivore numbers in check so they don’t overwhelm the plants. Bacteria and fungi make sure all that food keeps being recirculated in the ecosystems through decomposition (rot).

In ecosystems with high species diversity, several species compete or complement each other over the same niche. So if one pollinator species can’t perform the task, another one is there to pick up the slack. This makes the ecosystem as a whole more stable and resilient.

Crop fieds are a type of artificial ecosystem, but they’re much less robust than natural ones.
Image via Pixabay.

The next level is ecosystem diversity. Just like different species intermingle in an ecosystem and have particular roles, ecosystems interact with one another. If you think of the Earth as a huge ecosystem, then the sum of each of these ‘local’ ecosystems needs to perform a certain threshold of jobs (ecosystem services) for the whole system to be viable. For example, if there aren’t enough net-oxygen-generating ecosystems to supply all the demand for the gas, animals will start dying left and right. If there aren’t enough ecosystems to filter water, recycle nutrients, suck up carbon dioxide or other pollutants, and everything else that life needs, then the Earth will be downsizing on said life.

Where climate warming comes in

Species go extinct all the time, that’s just how life rolls. Generally, however, this natural or baseline rate of extinction is easily absorbed by ecosystems at large. Existing species cover now-free niches, or new species altogether evolve to exploit the opportunity.

From a biodiversity point of view, the issue with climate change is how fast it’s driving species extinct. Species go extinct when they fail to adapt to their environment or their competition. While natural processes can drive pretty fast and dramatic changes (think of how a meteorite impact killed the dinos and made mammals reign), most of the time they’re pretty gradual, which gives species some time to adapt or evolve to suit the present conditions. Natural changes, in general, also tend to impact a relatively limited area.

Global mean temperature anomalies (with 1951-1980 mean temperatures as baseline) between 1850-2017 as reported by Berkeley Earth, a California-based non-profit research organization.
Image credits Berkeley Earth.

Man-made climate warming is very fast — blisteringly fast from a geological point of view. The root of the issue is that our emissions are changing environments (this is the thing life needs to adapt to) way, way, way faster than biological evolution works. It also impacts the Earth in its entirety, affecting all ecosystems at the same time — so there aren’t any ‘unburdened’ ones to pick up the slack for those that are struggling since they’re all struggling.

To push the metaphor full circle, we’re closing the jobs in manufacturing and opening up new ones only in programming in the equivalent of a few hours, but programming school takes a few years to complete and very few people already know how to do it. Our way of life is driving the global economy — all of it — into a deep recession. The risk is that, by the time we take action to stop it, all the species that know how to manufacture the things we need to survive will be dead.

Hopefully, this handy guide helps you get a better idea of what biodiversity is and why it’s important. The world is a beautiful place, but we need to understand that it’s built on very complex and often fragile relationships. We need to make room and opportunity for these relationships to unfold, or we risk the world adapting to us — and wake up in a world that we’re no longer adapted for.

And we all know what nature likes to do to the species that can’t adapt, don’t we?


Climate change and ozone layer holes form feedback loop, reports international panel

The frays in our planet’s ozone layer are leading to changes in the planet’s climate and ecosystem, new research shows.


Image via Pixabay.

Increased solar radiation levels, a consequence of damage to the ozone layer, are causing shifts in the climate which impact the Earth’s natural systems. These changes affect everything from weather to the health and distribution of sea life according to the study’s authors, members of the United Nations Environment Programme’s Environmental Effects Assessment Panel, which informs parties to the Montreal Protocol.

No-ozone zone

“What we’re seeing is that ozone changes have shifted temperature and precipitation patterns in the southern hemisphere, and that’s altering where the algae in the ocean are, which is altering where the fish are, and where the walruses and seals are, so we’re seeing many changes in the food web,” said Kevin Rose, a researcher at Rensselaer Polytechnic Institute who serves on the panel and is a co-author of the review article.

The 1987 Montreal Protocol on Substances that Deplete the Ozone Layer, often shorthanded as the ‘Montreal Protocol’, was the first ever multilateral environmental agreement ratified by all members of the United Nations. Its aim was to protect Earth’s ozone layer (which acts like a kind of planetary sunscreen, blocking UV radiation) by phasing out harmful handmade substances, most notably the chlorofluorocarbons class of refrigerants. All in all, the Protocol was a success, and total mean ozone levels are on track to recover to pre-1980s levels by the middle of this century.

Earlier this year, however, researchers reported detecting new emissions of ozone-depleting substances from East Asia, which could throw a wrench into the plan.

The link between ozone depletion and an increase in UV levels on the Earth’s surface is well known and well documented. However, the effect it has on climate isn’t. In fact, we’ve only recently wisened up to the fact that climate is also affected by ozone depletion. The current paper focuses on the Southern Hemisphere, where a hole in the ozone layer is currently centered around Antarctica.

The increased levels of UV radiation passing through this area have pushed the Antarctic Oscillation — the north-south movement of a wind belt that circles the Southern Hemisphere — further south than it has been in roughly a thousand years, the team reports. This shift is directly fueling climatic changes in the Southern Hemisphere, they add.

In effect, the hole is causing climate zones to shift southward, affecting rainfall patterns, sea-surface temperatures, and ocean currents across large areas of the southern hemisphere. For example, some areas of the oceans have become cooler and more productive, while others have warmed up and lost productivity.

These changes domino into terrestrial and aquatic ecosystems from Australia, New Zealand, Antarctica, South America, Africa, and the Southern Ocean. Warmer oceans are linked to declines in Tasmanian kelp beds and Brazilian coral reefs, and the ecosystems that rely on them. Cooler areas have helped some populations of penguins, seabirds, and seals, who now have more krill and fish to feed on.

Rose also points out to feedback loops linking climate to UV radiation. Higher concentrations of atmospheric CO2, for example, have increased overall ocean acidity. Acid attacks calcium carbonate, the main component of shellfish shells, which renders these animals more vulnerable to UV radiation. Even us, he adds, are likely to wear lighter clothes in the warmer atmosphere we’re creating, making ourselves more susceptible to damaging UV rays. Furthermore, the team found evidence that climate change is also impacting the ozone layer and its recovery.

“Greenhouse gas emissions trap more heat in the lower atmosphere which leads to a cooling of the upper atmosphere. Those colder temperatures in the upper atmosphere are slowing the recovery of the ozone layer,” Rose said.

As one of three scientific panels to support the Montreal Protocol, the Environmental Effects Assessment Panel focused in particular on the effects of UV radiation, climate change, and ozone depletion. Thirty-nine researchers contributed to the article. Rose, an aquatic ecologist, collaborated with the aquatic ecosystems working group, which is one of seven working groups that are part of the panel.

The paper “Ozone depletion, ultraviolet radiation, climate change and prospects for a sustainable future” has been published in the journal Nature Sustainability.

Plant soil.

What is soil? Here’s the inside scoop

Ground beneath your feet — all planets have it (yes even gas giants). But the one on our Earth is a little different from those in other places. So, what exactly is soil, and what makes ours stand out?

Plant soil.

Image via Pixabay.

Soils are actually very complex things. They’re a mix of solid material — both organic and inorganic — with fluids such as water and air, with a helping of living organisms thrown in to tie everything together. It’s a very dynamic material, one that responds to factors such as climate, terrain, biology, and human activity to name a few. It’s also continuously developing. Depending on where on Earth you look, and when, soils take on unique properties. It’s so complex, in fact, that soils are treated as ecosystems unto themselves.

However, life as we know it would be impossible without soil. So, everybody, grab your spades and let’s take a look at what exactly soil is.

The most bare-bones definition of soil is that it is a mixture of sand, clay, silt, and humus (not the tasty spread). In more geologically-savvy talk, soil is the unconsolidated mineral and/or organic material that forms on the immediate surface of the Earth. According to the Soil Science Society of America Glossary of Soil Science Terms, soil is also “subjected to and shows effects of genetic and environmental factors of: climate (including water and temperature effects), and macro- and microorganisms, conditioned by relief, acting on parent material over a period of time.” In other words, soils represent a mixture of geology and biology, and they are, quite literally, the substrate that fosters life on dry land.

The inorganic parts



Sand is not readily carried by water.
Image credits Andrew Martin.

The ‘geology’ part includes the inorganic elements of soil — mainly ground-up, weathered rocks and minerals. Weathering are the mechanical or chemical processes through which rocks are broken down into smaller pieces. These rocks and minerals are referred to as the soil’s “parent material“. This inorganic fraction represents around 90% by volume of all the solid material in the mix.

Soil texture is mainly produced by the ratios of different types of inorganic material in the soil. We generally classify these by the size of their particles. The three main types are sand, silt, and clay.

Sand is the coarsest of the three, with particles ranging in diameter from 0.0625 mm to 2 mm. Soils that contain more than 85% sand-sized particles by weight are called sand. Its exact composition varies from place to place, but generally, sand is made up of silica (quartz).

Particles in sand are pretty loose and coarse which creates a lot of open spaces for water to flow through. This makes sand very good at draining and filtering water. Its lack of organic material and inability to hold water, however, makes it a very poor environment for plants to grow in.

Silty water.

Silt is easily mixed with water because of how light its particles are, and can be carried over great distances.
Image credits Andrew Martin.

Silt is an intermediate texture, with particles ranging between 0.0039 mm and 0.0625 mm in diameter. To give you a rough idea, dry silt feels like coarse flour in your hands. Add water to it, and it would feel smooth, almost silky to the touch, without being sticky. Silt is much better than sand at holding in water. Due to its smaller-sized particles, it can be transported over long distances by wind (forming loess) or rivers. It is composed mainly of quartz and feldspar.

Silt an important component for fertile soils. Because of the size of its particles, it’s good at holding water for plants to absorb through their roots, but also creates enough open spaces for air pockets to form (more on that later). Smaller particles also mean they can be circulated around an environment to provide fresh minerals for plants. The Nile River, for example, brings huge amounts of fresh silt, rich in organic material, to bear on its banks every time it floods; this has single handedly fed Ancient Egypt’s ascent in the middle of an inhospitable desert. It had such a central role to play in the Egyptians’ life that they adopted the black silt on the Nile’s banks as a symbol of rebirth.


Clay can absorb a lot of water — and all that water increases its volume. Clay contracts and breaks apart when it dries and sheds those water molecules.

Clay is the finest type of material on the list. Its texture feels like that of eye shadow. While the exact point at which a particle is no longer considered silt varies depending on which discipline you’re asking, geologists usually consider particles under 2 micrometers to be clay. It’s usually made up of metallic oxides, which make clay quite colorful. These oxides are why clay-fired bricks are red, but clay can come in a wide range of colors.

Clays are made of wide, flat particles — which means that they have large surface areas compared to the other inorganic fractions. This makes them more chemically active than silt or sand and thus, better able to hold nutrients onto their surfaces. As such, clays can help make very fertile soils. Too much clay, however, can dry plants out — clay particles are good at capturing water but not very good at letting it go.

Overall, the inorganic components of soil mainly include silica, with iron and aluminum oxides. They mainly create soil’s texture and structure. Overall, it isn’t of much value to plants, although fractions like clay can transport nutrients.

The organic parts

Apple soil.

Image credits Annette Meyer.

Geology alone isn’t enough to produce soil. Mars, too, has a lot of ground-up, weathered rocks and minerals about its surface. So does the moon — but that’s just barren dirt. The components that set ‘soil’ apart from ‘dirt’, the bits that give it its unique pizzaz, are biological. Soil is pretty dense in organic material, which makes up around 10% of the volume of its solid components. The two main types of organic matter in soil are the living and the non-living fractions.

The latter improves soil’s ability to hold water, improves its nutritive value, and helps form stable aggregates (i.e. it ties everything together). It mostly originates from the microbial decomposition of animal or plant material (such as leaves, roots, soft tissues, or feces). This breakdown process recirculates nutrients through the soil to feed plants. Exactly how fast this material breaks down depends on how homey the soil is for bacteria. Higher decomposition rates occur in warm, moist conditions with good aeration, a favorable ratio of nutrients, with a pH (soil acidity) near neutral, and without pollutants or toxins.

Organic matter content in soil depends on how much of it is added versus how much of it is broken down over a given unit of time. Bacteria first munch on the juicier bits, such as sugars, starch, and certain proteins. More resistant compounds — such as the structural components in cell walls — are decomposed relatively slowly. These compounds, such as lignin and tannin, impart a dark color to soils containing a significant organic matter content. In general, the darker the soil, the more organic material it contains — so the better it is for growing plants.


Compost is just organic material slowly breaking down into soil.
Image credits Manfred Antranias Zimmer.

Living organic matter includes the aforementioned bacteria, earthworms, and everything in between. Fungi, actinomycetes, algae (yes, there is algae in soil), and protozoa also make an appearance. These organisms all work together to make soil the complex ecosystem it is, but they can both support and hinder plant growth. They can help plants by decomposing organic matter, fixing nitrogen (which plants can’t do themselves), and by improving soil quality through aggregation, aeration, and drainage. On the other end of the spectrum, they can compete with plants for nutrients or munch on their roots.

Soil structure

Soil profile.

Its a layered dirt cake!
Image credits Colin Smith.

Soils have complex structures to go along with their complex makeup. Dig down through some and you’ll see it’s made of layers, which are also called ‘horizons’. Taken together, all of these horizons form a soil’s profile. As a rule of thumb, almost all soils have three major horizons, and most also have an organic horizon. In order, a soil’s profile can include:

  • An organic/humus horizon. This material is mostly made up of organic matter in various stages of decay. If you’ve ever walked through a thick forest in spring, you may have noticed that there’s a brown, wet, mushy layer of something between the fallen leaves of last year and the ground proper. That’s plant matter that is rapidly being turned into soil and is part of this organic horizon. This layer shows great variation between soils: it’s thin in some, thick in others, and completely absent in some cases.
  • Topsoil. This horizon is mostly made up of minerals from the soil’s parent material mixed in with a healthy heaping of organic matter. It’s a very cozy place, and most plants and animals that live in soil call this layer home.
  • The eluviated horizon. This is a blanket of gravel, sand, and silt particles of quartz or other particularly hardy materials left over after the clay, organic matter, and more soluble minerals have been washed away by water draining through the soil. It has to be noted that water does this to the above horizons as well, but those tend to be replenished through organic decomposition. The eluviated horizon isn’t seen in most soils but is quite often found in older soils and forest soils.
  • The subsoil. This part is packed with minerals and nutrients washed down from the above layers that get stuck here like coffee grounds onto filter paper.
  • Parent material. The inorganic ‘foundation’ from which the soil developed.
  • The bedrock. A solid mass of solid rocks (usually granite, basalt, quartzite, limestone, or sandstone). If the bedrock is close enough to the surface to weather, it can serve as the parent material for the above soil. But, make no mistake — this is rock. This bit isn’t considered soil.

A lot of this column, ideally, is empty air. Fertile, medium-grain soils can reach up to 50% porosity, and all this empty space is crucial for its health. The pores allow air and water to pool and (ideally) circulate through the soil, keeping both its flora and fauna alive.

Pore size (which is dictated by particle size) is important, too, as is the distribution of these pores. If a pore is too small, it traps water too tightly for plants to absorb. That’s why soils with a large clay content aren’t very good for agriculture. We till the land as a way to break it up and temporarily increase its porosity and permeability.

Pores that are too large just let water woosh right through, as we discussed earlier, which is just as bad for plants. Large pores that communicate (i.e. that are connected) with one another allow water and air to move freely through the soil, carrying nutrients around. However, smaller pores are better if you’re dealing with drought — they store water better.

As far as flora is concerned, pores can keep different populations of bacteria separate from one another. This is actually pretty good news since it keeps the strains from competing with one another directly. As such, soil porosity allows for multiple organisms that occupy the same ecological niche to coexist, which improves its resilience to shocks such as pollution or climate change.

It’s easy to take the soil under our feet for granted — after all, it’s just dirt in our soles. But hopefully, I’ve helped you see a glimpse of the living, breathing ecosystem that underpins all of the life on dry land, and most of the life on Earth. So the next time you visit the park, spare a moment to think of all the hard work that’s going on beneath your shoes — we wouldn’t be here without it.

Peltigera aphthosa.

Arctic plants are getting taller due to climate change — which could fuel more climate change

Throughout the southern reaches of the Arctic, plants are getting taller due to climate change.

Peltigera aphthosa.

The common freckle pelt lichen (Peltigera aphthosa) is often found on mossy ground, rocks, or under trees in Arctic ecosystems.
Image credits James Walton / NPS.

While not graced with the lush vegetation of the Earth’s other areas, the Arctic is far from desolate. Hundreds of species of low-lying shrubs, grasses, and other plants make a home in the frigid expanse, and they play a key role in the carbon cycle. However, anthropic climate change is causing new plants to move into the Arctic’s southern stretches which, according to a new paper, can lead to quite a bit of hassle in the future.

Growing (too) strong

An international team of 130 researchers, led by Dr Isla Myers-Smith of the School of Geosciences at the University of Edinburgh, and Dr Anne Bjorkman from the Senckenberg Biodiversity and Climate Research Centre (BiK-F) in Frankfurt, has been investigating the Arctic flora as part of a Natural Environment Research Council (NERC)-funded project.

The team looked at more than 60,000 data points from hundreds of sites across the Arctic and alpine tundra and report that higher mean temperatures are impacting the delicate balance of these ecosystems. This is the first time that a biome-scale study looking at the role plants play in this rapidly-warming part of the planet has been carried out, says Bjorkman.

“Rapid climate warming in the Arctic and alpine regions is driving changes in the structure and composition of plant communities, with important consequences for how this vast and sensitive ecosystem functions,” Dr Bjorkman adds.

“Arctic regions have long been a focus for climate change research, as the permafrost lying under the northern latitudes contains 30 to 50 percent of the world’s soil carbon”.

Among other things, plants insulate the soil they grow in from incoming sunlight. While this is rather fortunate for us during a hot summer’s day, in the Arctic, it’s a matter of ecosystem stability. Taller plants also help to trap more snow beneath their leaves. This thicker blanket of snow, in turn, further insulates the soil from temperature changes in the atmosphere, preventing it from freezing.

In other words, taller plants in the Arctic keep soil thawed for more days each year, leading to “an increase in the release of greenhouse gases” as biological matter trapped in the soil has a wider window of time annually to decompose.

“If taller plants continue to increase at the current rate, the plant community height could increase by 20 to 60 percent by the end of the century,” Dr Bjorkman explains.

The team gathered their data from sites in Alaska, Canada, Iceland, Scandinavia, and Russia. Alpine sites in the European Alps and Colorado Rockies were also included in the study. For each dataset, the team looked at the relationship between temperature and soil moisture. They also tracked plant height and leaf area, along with specific leaf area, leaf nitrogen content, leaf dry matter content, as well as ‘woodiness and evergreenness’.

Out of all these characteristics, only height increased meaningfully over time. Temperature and moisture levels (which is strongly affected by temperature) had the strongest influence on observed plant characteristics.

“We need to understand more about soil moisture in the Arctic. Precipitation is likely to increase in the region, but that’s just one factor that affects soil moisture levels,” Dr Myers-Smith said. “While most climate change models and research have focused on increasing temperatures, our research has shown that soil moisture can play a much greater role in changing plant traits than we previously thought.”

The results suggest that (through the mechanism explained previously), this increase in overall plant height could have significant implications for both the Arctic and the world at large. At the same time, they should help us better tailor our climate models, to take into account increased greenhouse gas emissions from the area.

The paper “Plant functional trait change across a warming tundra biome” has been published in the journal Nature.


Climate change will become the leading cause of vertebrate-species loss by 2070

Over the next few decades, climate change will overtake habitat destruction as the main threat against biodiversity, a new study warns.


Image credits Anja Osenberg / Pixabay.

Long-time readers know that we at ZME Science think climate change is a huge threat to the planet and our place in it. It’s a position that draws a fair share of heckles in the comments and emails, accusing us of fearmongering and of being ‘leftists’ — quite confusingly so, since (almost) the whole team is right-handed. Regardless, ‘it’s not true’, they say. ‘It’s all a Chinese hoax’, presidents bellow. Presumably, one designed to steal ‘ar jawbs, somehow.

I’m quite sad to say that these hecklers may have, partially, been right. New research shows that climate change isn’t a huge threat — it is, in fact, quickly becoming the threat against ecological systems.

Climate change, ecological change

The effects of climate change on the structure of ecosystems across the globe will rapidly increase over the next few decades, says Dr. Tim Newbold from the University College London. This will eventually see climate change become the leading cause of biodiversity loss, outstripping vertebrate loss rates caused by land use and habitat destruction. Amphibians and reptiles will be more significantly affected than birds and mammals, he adds.

Today, human land use is responsible for an estimated 10% of the losses in overall biodiversity.

It’s quite a worrying figure. Research has previously found that an ecosystem will start to break down when around 20% of its member species are lost. That threshold has already been passed on more than 25% of the world’s surface, or around 60% when roads are also taken into account.

Newbold’s study shows that climate change will exceed the effects habitat destruction has on vertebrate biodiversity by 2070. These results suggest that our best bet to maintain ecological integrity is taking both anthropic land use and climate change into account, instead of just focusing on one of the two. It’s the combined effects that pose the greatest threat, the paper notes.

“This is the first piece of research looking at the combined effects of future climate and land use change on local vertebrate biodiversity across the whole of the land surface, which is essential when considering how to minimise human impact on the local environment at a global scale,” says Dr. Newbold.

“The results show how big a role climate change is set to play in decreasing levels of biodiversity in the next few decades and how certain animal groups and regions will be most affected.”

The paper also estimated that vertebrate communities will lose between 10% to over 25% of species on a local level as a result of climate change. When combined with the effects of land use, such communities could lose between 20% to 40% of their members by 2070.

As different areas and ecosystems respond in different ways to climate change, the latter’s effects won’t be evenly distributed — that’s why Newbold’s estimations vary in so large an interval. Tropical rainforests are likely to experience major losses, while temperate regions (the most affected by land use) will likely see relatively small biodiversity losses. Tropical grasslands and savannahs are also expected to see strong loses, Newbold adds, as result of both climate change and human activity.

The paper “Future effects of climate and land-use change on terrestrial vertebrate community diversity under different scenarios” has been published in the journal Proceedings of the Royal Society B.

Limiting global warming to 1.5 degree C would save most global species, new study concludes

If we manage to keep global warming within 1.5 degrees Celsius (the ambitious goal of the Paris Agreement), then we can save the vast majority of the world’s plant and animal species from climate change, a new analysis concludes.

The American pika is considered an indicator species for detecting ecological effects of climate change in mountainous regions. Image credits: NPS.

The world is heating up — it’s no longer a case of if this is happening, but rather how fast can we limit the damage. Two realistic scenarios are that we limit global warming to 2C (2 degrees Celsius) or 1.5C. These are also the goals of the international Paris Agreement: countries have pledged to play their part to limit global warming to 2C, and have also agreed on the extended 1.5C goal.

Most previous studies have focused on how ecosystems will behave at 2C, and few (if any) have focused on insects — insects are often neglected or understudied, even though they offer vital ecosystem services such as pollinating crops and flowers and serve as part of the food chain for other birds and animals.

Now, a new study has analyzed the more optimistic scenario, and also focused on insects. Researchers at University of East Anglia in the UK and James Cook University in Australia studied some 115,000 species including 31,000 insects, 8,000 birds, 1,700 mammals, 1,800 reptiles, 1,000 amphibians and 71,000 plants. Their conclusions are intriguing, and mostly optimistic. Lead researcher Prof Rachel Warren, from the Tyndall Centre for Climate Change Research at UEA, said:

“We wanted to see how different projected climate futures caused areas to become climatically unsuitable for the species living there. We measured the risks to biodiversity by counting the number of species projected to lose more than half their geographic range due to climate change.”

“We found that achieving the ultimate goal of the Paris Agreement, to limit warming to 1.5C above pre-industrial levels, would reap enormous benefits for biodiversity – much more so than limiting warming to 2C.”

Importantly, insects will particularly benefit if the upper climate change limit is 1.5C instead of 2C. Of course, things would still not be good, but the brunt of the damage would be averted.

“Insects are particularly sensitive to climate change. At 2C warming, 18 per cent of the 31,000 insects we studied are projected to lose more than half their range. This is reduced to 6 per cent at 1.5C. But even at 1.5C, some species lose larger proportions of their range.”

However, that’s a big if. Countries agreed to try and limit emissions, keeping warming down to 2C, but not everyone agrees that that will be enough — some scientists argue that following the Paris Agreement won’t do nearly enough to reach its objective. Furthermore, the situation is complicated by President Trump’s announcement to take the US out of the Paris Agreement. Even if all these things fall into place, we will still be at 2C, not 1.5C, so we would still need more.

“The current global warming trajectory, if countries meet their international pledges to reduce CO2, is around 3oC. In this case, almost 50 per cent of insects would lose half their range.”

“This is really important because insects are vital to ecosystems and for humans. They pollinate crops and flowers, they provide food for higher-level organisms, they break down detritus, they maintain a balance in ecosystems by eating the leaves of plants, and they help recycle nutrients in the soil.”

Ultimately, it won’t be just the biodiversity that suffers, but ourselves as well.

“If temperatures rise by 3oC, ecosystem services provided by insects would be greatly reduced. Other research has already shown that insects are already in decline for other reasons, and this research shows that climate change would really compound the problem.”

Journal Reference: ‘The projected effect on insects, vertebrates and plants of limiting global warming to 1.5oC rather than 2oC’ is published in the journal Science on May 18, 2018.

Credit: Wikimedia Commons.

Scientists successfully transplant coral into the devastated Great Barrier Reef

Credit: Wikimedia Commons.

Credit: Wikimedia Commons.

In a bid to save the endangered Great Barrier Reef from the effects of man-made pollution and climate change, Australian scientists have turned to desperate measures. They’ve first bred baby corals in an artificial environment and later moved them to some of the most damaged parts of the reef. Eight months later, the juvenile coral had survived and grown, lending hope that such measures can restore similarly damaged ecosystems, not just in the Great Barrier Reef, but around the world as well.

“The success of this new research not only applies to the Great Barrier Reef but has potential global significance,” lead researcher Peter Harrison of Southern Cross University said in a statement.

“It shows we can start to restore and repair damaged coral populations where the natural supply of coral larvae has been compromised.”

Scientists led by Harrison traveled to the reef’s Heron Island off Australia’s east coast where they collected egg and sperm late last year. About a million larvae were grown, with more than 100 surviving and growing successfully on a settlement tile on the reef, aided by underwater mesh tanks.

The new technique could be the answer to some of the problems that plague the Great Barrier Reef, which has declined by more than half in the last 30 years. The main reason is climate change; warming waters and its increasing acidity from CO2 inputs are pushing the reefs past the point of no return. One recent study found that about a third of the central and northern regions of the Great Barrier Reef has died due to a huge bleaching event. Corals to the north of Cairns, which account for two-thirds of the Great Barrier Reef, are also massively affected with 35 to 50 percent dead or dying. Bleaching occurs when the ocean’s waters become too warm: heat stress makes the corals expel their photosynthetic algae, called zooxanthellae, with which they live in a symbiotic relationship. Without the algae, the coral dies and seaweeds take over.

Previously, conservationists have used other methods to restore the Great Barrier Reef such as “coral gardening”, which involves breaking up healthy coral and sticking healthy branches on the reef. Harrison is more optimistic about his approach which was earlier demonstrated around the Philippines, in areas degraded by blast fishing.

“The results are very promising and our work shows that adding higher densities of coral larvae leads to higher numbers of successful coral recruits,” he added.

The news is like a breath of fresh air. The Great Barrier Reef, which is the largest living structure on Earth, is reeling from the second year straight of coral bleaching due to climate change. The success of these first trials are very encouraging, but the accelerated rate of coral decline in the reef is staggering. The challenge will be figuring out how to broaden the scale of coral breeding and transplant technology to really make a difference.

At the end of the day, coral transplants can only patch reefs. It’s like a pill that treats symptoms instead of the underlying illness, which actually causes the symptoms. Like any coral, the transplant variety will also be subjected to bleaching. If we’re to save the Great Barrier Reef and other ecosystems in a similar situation, the only viable solution is to urgently cut back on fossil fuel use and greenhouse gas emissions.

Orange peel dump.

Juice company dumped orange peels in Costa Rican national park in the 90s — it revived the forest

Back in the 1990s, a husband and wife duo of University of Pennsylvania ecologists teamed up with a juice company to dump orange peels and pulp on a barren pasture in a Costa Rican national park. Today, the area is covered in lush vegetation that puts neighboring forests to shame, a new paper reports.

Orange peel.

Image credits Myriam / Pixabay.

This project is the brain child of Daniel Janzen and Winnie Hallwachs, a husband-and-wife team of ecologists at the University of Pennsylvania who worked as researchers and technical advisers for Costa Rica’s Área de Conservación Guanacaste (ACG, Guanacaste Conservation Area) back in the 90s. The job let them witness the strain tropical forest ecosystems are put under first-hand — so they decided to focus the latter half of their careers on preserving them.


So in 1997, they approached orange juice manufacturer Del Oro, a company that was just starting production along the ACG’s northern border with a proposal. If Del Oro would donate a part of the forested area they owned to the ACG, it would be allowed to dump its orange waste at no extra cost on degraded land within the park. The deal went through and in the first year alone some 12,000 metric tons of orange pulp and peels found their way to degraded land. Because of legal complications (a rival company sued Del Oro for “defiling a national park”), the peeled land remained largely overlooked up to now.

But the deal did pay off, says Timothy Treuer, a graduate student in Princeton’s Department of Ecology and Evolutionary Biology and co-lead author of the paper quantifying the outcome today.

Orange peel dump.

We’re talking a lot of oranges here.
Image credits Daniel Janzen and Winnie Hallwachs.

“This is one of the only instances I’ve ever heard of where you can have cost-negative carbon sequestration,” Treuer adds. “It’s not just a win-win between the company and the local park — it’s a win for everyone.”

Truer teamed up with Jonathan Choi, who was a Princeton ecology and evolutionary biology senior at the time. The two evaluated two sets of soil samples to see what (if any) effect the peels had on soil quality. The first set of samples was collected and analyzed in 2000 by co-author Laura Shanks from Belio College. Her results were never published, so her analysis was incorporated in the study to serve as a benchmark. The second set of samples was collected in 2014 by Choi.

But even without looking at the results, the duo could tell that the oranges left a big mark on the area.

“It was so completely overgrown with trees and vines that I couldn’t even see the 7-foot-long sign with bright yellow lettering marking the site that was only a few feet from the road,” Truer recounts.

“The site was more impressive in person than I could’ve imagined,” Choi added. “While I would walk over exposed rock and dead grass in the nearby fields, I’d have to climb through undergrowth and cut paths through walls of vines in the orange peel site itself.”

More of everything


Image credits Daniel Janzen and Winnie Hallwachs.

To quantify changes in vegetation, the team used several transects within the area. These were 100-meter-long parallel lines through the forest, which the team would use as guides. For control, they set up a similar transect system on the pasture on the other side of the road, which hadn’t been used to dump the peels.  Lastly, they identified the species and measured the diameter of every tree within 3 meters of each transect for both areas.

The differences were quite dramatic. In the peel-plastered area, the team found richer soil, more diversity in the species of trees, more overall biomass (the trees grew bigger and faster), and greater canopy closure compared to the control area.

They found dramatic differences between the areas covered in orange peels and those that were not. The area fertilized by orange waste had richer soil, more tree biomass, greater tree-species richness and greater forest canopy closure. All in all, these effects show that agricultural waste can play a huge hand in regenerating forest ecosystems while also sequestering a large quantity of carbon at virtually no cost to industry or society at large.

“Plenty of environmental problems are produced by companies, which, to be fair, are simply producing the things people need or want,” said study co-author David Wilcove, Professor of ecology and evolutionary biology and public affairs and the Princeton Environmental Institute.

“But an awful lot of those problems can be alleviated if the private sector and the environmental community work together. I’m confident we’ll find many more opportunities to use the ‘leftovers’ from industrial food production to bring back tropical forests. That’s recycling at its best.”

It’s not very surprising to see that the peels helped the forest get back on its feet — after all, people have been using compost to fuel crops for centuries. Considering the ease and virtually inexistent cost of the operation, however, similar projects should be implemented around the world to boost struggling forest ecosystems while keeping our landfills emptier.

The paper “Low-cost agricultural waste accelerates tropical forest regeneration” has been published in the journal Restoration Ecology.


Pristine mountain habitats are also not safe from climate change

Incoming climate change will have a drastic effect on pristine mountain habitats across the world, a new study has found.

Image credits: U.S. Fish and Wildlife Service.

As we’ve mentioned so many times before, no corner of the Earth will be left untouched by global warming. A new study by University of Manchester researchers which spanned seven major mountain regions of the world revealed that decreasing elevation – descending a mountainside to warmer levels – is an excellent proxy for studying climate change. Basically, this acts as a ‘surrogate’ indicator of climate warning and is very useful for simulating what will happen when the climate changes. What they found is that rising temperatures will create a mismatch between soils, plants, and other ecosystem actors. This will have a cascade effect and will be felt across the entire ecosystem.

Manchester ecologist Professor Richard Bardgett, who was part of the international team that initiated and designed the study, explains:

”A clear message from our findings is that climate warming could change the functional properties of mountain ecosystems and potentially create a disequilibrium, or mismatch, between plants and soils in high mountain areas.

“Not only could this have far reaching consequences for biogeochemical cycles but it could also affect mountain biodiversity.”

Basically, changing temperatures are affecting nutrient availability in soils. This, in turn, affects the plants and the soil’s microbial communities. This perturbs the very base of the ecosystem and the entire food chain. Professor Bardgett, based in Mancheser’s School of Earth and Environmental Sciences, added:

“Mountain areas cover a large part of the Earth’s land surface and are very vulnerable to climate change.”

It’s not a secret that mountain areas are vulnerable to climate change, but this is the most comprehensive study of its kind to date, and it also involves a more innovative approach. Instead of using short term or localized experiments, they analyzed real places above and below the alpine line (the highest elevation at which trees still survive) in many parts of the world, in many different types of environments. Bardgett adds:

”Our results, which come from an extensive study of elevation gradients across seven mountain regions of the world – including Japan, British Columbia, New Zealand, Patagonia, Colorado, Australia, and Europe – suggest that future climate warming will substantially alter the way that these sensitive ecosystems function.”

Interestingly, despite all these different areas (which include different soils and different types of ecosystems), results were quite similar: the effects of climate change are far-reaching and long lasting. From the lowest field to the tallest mountain, we’ll feel it everywhere.

“What we found was remarkably consistent across the different mountain regions of the world. Our results not only suggest that warming could impact the way that plants grow in mountain ecosystems, but also that these changes are linked to effects of warming on soils, especially the cycling of key nutrients that sustain the growth of plants.”

It’s extremely unlikely that the ecosystems would manage to adapt to these changes. Shifts of 1 or 2 degrees are not uncommon on geological scales — but geological scales are hundreds of thousands and millions of years, while this is centuries we’re talking about. Birds can’t completely change their migration routes, and old trees can’t shift to changing soil conditions. If the ball gets rolling, it’s not stopping.

The findings are published in the journal Nature in a paper entitled ‘Elevation alters ecosystem properties across temperate tree lines globally’.

The Mexican grizzly bear became extinct in 1964. Credit: Wikipedia

Humanity is driving thousands of species extinct, but there’s a flip side — we also create new species

The Mexican grizzly bear became extinct in 1964. Credit: Wikipedia

The Mexican grizzly bear became extinct in 1964. Credit: Wikipedia

We’re all used to the depressing headlines of yet another species having gone extinct (or is just about to) due to human interference. Logging, pollution, hunting, urban expansion — these and much more take their toll on wildlife and only a select few can adapt.

Sometimes, though, humans can act as a prime driver for speciation. One example includes a new species of mosquito that dwells in the undergrounds of London and can’t breed with mosquitos that fly at the surface. It’s an entirely new species, shaped by an ecosystem that we created.

The  ‘London Underground mosquito’ is not alone, as other examples are plentiful. Writing in a new report titled ‘How humans drive speciation as well as extinction’, two researchers discuss the mechanisms that drive the formation of human-mediated speciation.

The London Underground Mosquito, found in underground systems worldwide. Presumed to have evolved from standard house mosquito. (Credit: Wikimedia Commons)

The London Underground Mosquito, found in underground systems worldwide. Presumed to have evolved from standard house mosquito. (Credit: Wikimedia Commons)

There are around five to eight million eukaryotic species living on this planet, and 1.0–2.2% of these species become extinct every decade or so. At this rate, many scientists warn, the world is headed for a sixth mass extinction — the only one that won’t be caused by nature. Humans are the obvious culprit, but the authors of the new study say humans also drive the formation of new species. They argue that there are various ways that mediate this process, like human induced physical barriers or selective pressures applied to specific members of a species.

“The prospect of ‘artificially’ gaining novel species through human activities is unlikely to elicit the feeling that it can offset losses of ‘natural’ species. Indeed, many people might find the prospect of an artificially biodiverse world just as daunting as an artificially impoverished one” study author Joseph Bull from the Center for Macroecology, Evolution and Climate at the University of Copenhagen, said in a statement. 

Of course, the most obvious way humans create new species is through domestication. Since the advent of agriculture 8,000 years ago countless species of plants, be them crops or flowers, have been selected and interbred until they look and behave nothing like the original wild species. Wild boars became pigs, wolves became dogs, and “at least six of the world’s 40 most important agricultural crops are considered entirely new” explains Joseph Bull.

[panel style=”panel-info” title=”Humans shaping extinction and speciation alike” footer=”Center for Macroecology, Evolution and Climate Dept. of Food and Resource Economics University of Copenhagen”]Since the last Ice Age, 11.500 years ago, it is estimated that 255 mammals and 523 bird species have gone extinct, often due to human activity. In the same period, humans have relocated almost 900 known species and domesticated more than 470 animal and close to 270 plant species.[/panel]

While domestication is deliberate, most new species which the researchers have identified as being speciated by human activity are the result of unnatural selection. Hunting, for instance, can lead to the adaptation of new traits in animals, which eventually leads to new species. Relocating species, either deliberately or by accident, can also lead to the hybridization of species. In the last three centuries in Europe, at least, due to the relocation of species more new plant species have appeared than those who went extinct.

Then, of course, we have the most disruptive human-driven speciation mechanism: the creation of entirely novel ecosystems. Humans have built cities, farms and underground railways like the one the new mosquito species calls home. Finally, the researchers note that technology might drive more speciation than ever before. Examples include genetically modified organisms, which although are not new species may have the capacity to generate self-sustaining populations or hybridize with wild species. Technology may soon also allow re-creation of extinct species (de-extinction), despite deep practical and moral arguments against doing so.

“In this context, ‘number of species’ becomes a deeply unsatisfactory measure of conservation trends, because it does not reflect many important aspects of biodiversity. Achieving a neutral net outcome for species numbers cannot be considered acceptable if weighing wild fauna against relatively homogenous domesticated species. However, considering speciation alongside extinction may well prove important in developing a better understanding of our impact upon global biodiversity. We call for a discussion about what we, as a society, actually want to conserve about nature”, says Associate Professor Martine Maron from the University of Queensland.

The takeaway is that any species gone extinct at the hand of man is a tragedy. Millions of years of heritage lost forever (despite pipe dreams of cloning, de-extinction and what not). That being said, adding new species in the ecosystem, intentionally or unintentionally, does nothing to make things better. But one can only wonder, what would have biodiversity looked like today if humans lived more sustainably? We might never learn.

Are cephalopods taking over the oceans?

Human activity has been wreaking havoc on ocean life, but one group however seems to thrive where others struggle to survive. New evidence shows that cephalopod numbers have significantly increased over the last six decades.

Image via pixabay

Cephalopods such as squids, octopuses and cuttlefish have several traits that allow them to adapt much quicker than other ocean denizens: they grow really fast, have short lifespans and have a very sensitive phisique. These qualities have allowed them to thrive even as most other ocean creatures are declining in numbers.

Zoë Doubleday of Australia’s Environment Institute at the University of Adelaide and her team analyzed global cephalopod catch rates (catches per unit of fishing or sampling effort) from 1953 to 2013. The study included 35 species and genera from six families of cephalopods. Their results show that more and more of these creatures are ending up in fishing nets, all over the world. This suggests that they’re increasing in numbers.

“The consistency was the biggest surprise,” says Doubleday. “Cephalopods are notoriously variable, and population abundance can fluctuate wildly, both within and among species. The fact that we observed consistent, long-term increases in three diverse groups of cephalopods, which inhabit everything from rock pools to open oceans, is remarkable.”

While it is pretty neat to see how tenacious life can be, this increase can turn out to be a double-edged sword:

“Cephalopods are voracious and adaptable predators and increased predation by cephalopods could impact many prey species, including commercially valuable fish and invertebrates,” the team writes. “Conversely, increases in cephalopod populations could benefit marine predators which are reliant on them for food, as well as human communities reliant on them as a fisheries resource.”

Predicting exactly what this increase means for marine ecosystems and its socio-economic consequences is going to be difficult, the team admits. We don’t really know how fishing will affect this new state of ocean affairs, nor what’s driving the cephalopods’ proliferation. But the team plans to find out.

“It is a difficult, but important, question to answer, as it may tell us an even bigger story about how human activities are changing the ocean,” Doubleday concludes.

Video via Newsy

The full paper, titled “Global proliferation of cephalopods” has been published online in the journal Current Biology and can be read here.

Why don’t they just eat all of them – predator-prey study reveals new law governing ecosystems

The results of a new study offer insight into the workings of predator-prey mechanisms, more specifically how the number of herbivores and other animals that are preyed upon affect the number of carnivores.

Image via animalslook

McGill PhD student Ian Hatton, lead scientist of the paper, was on vacation when the idea of the study came to him:

“I went to high school in Zimbabwe and spent vacations in the National parks there,” he said. “When I began my PhD in biology at McGill, I wanted to go back and compare whole communities of African animals across protected ecosystems to see how the numbers of carnivores are related to their herbivore prey at the scale of whole landscapes. So I gathered all the animal census data I could for parks in east and southern Africa.”

The wildlife parks of Africa are teeming with tasty, tasty herbivores. So why aren’t there more lions, or more hyenas, to take advantage of the easy feast? One might imagine that the population of predators in each park would increase to match the available prey.

When Hatton and his colleagues started compiling the data and crunching the numbers, summing up all the carnivores (lion, hyena, leopard, etc.) and herbivores (buffalo, zebra, impala, etc.) in these parks, they found a very unexpected and regular pattern.

For every park they looked at, there seemed to be a very consistent relationship of predator to prey, but not in the one they might have expected to find.

Too crowded for romance

What the team discovered was that, across the board, prey reproduced less in crowded settings than they did when their numbers were smaller. They found this same pattern to be consistent with a whole range of different ecosystems. The team believe this to be the bottleneck that keeps predator populations in check ecosystem-wide.

Growth of the predator population seems to be kept in check by the rate of “food” reproduction in any given ecosystem. Image via eurasiareview

“Until now, the assumption has been that when there is a lot more prey, you’d expect correspondingly more predators,” said Hatton. “But as we looked at the numbers, we discovered instead, that in the lushest ecosystems, no matter where they are in the world, the ratio of predators to their prey is greatly reduced. This is because with greater crowding, prey species have fewer offspring for every individual. In effect, the prey’s rates of reproduction are limited, which limits the abundance of predators.”

It’s a surprising find, suggesting a level of structure and function in ecosystems that had not previously been recognized. Although biologists have long made use of very regular mathematical laws -governing functions in the body like metabolism and growth- to explain many of life’s processes, no study has ever shown that similar kinds of laws may exist at a global level. Some scientists are already suggesting that it may well be the discovery of a new law of nature.

Once they observed this pattern in one setting, the team began analyzing data about food pyramids, and the relationship between predators and prey in ecosystems from the Indian Ocean, the Canadian Arctic to the tropical rainforests. Over the course of the next few years they analyzed data gathered about both plants and animals from more than 1000 studies done over the past 50 years covering a range of grassland, lake, forest and ocean ecosystems around the world.

In all these different settings, they found a consistent relation between predators and prey, and confirmation that rather than the numbers of predators increasing to match the available prey, predator populations are limited by the rate at which prey reproduce.

“We kept being astonished,” said Kevin McCann, of Guelph University’s Department of Integrated Biology, one of the study’s co-authors. “This is just an amazing pattern.”

Probably not the kind of predators the study deals with. Probably.
Image via storiesbywilliam

Same rules, different sizes


What the researchers also found intriguing was that the growth patterns that govern whole ecosystems, where large numbers of prey seemed to naturally inhibit reproduction, were very similar to the patterns of growth in individuals.

“Physiologists have long known that the speed of growth declines with size,” said co-author Jonathan Davies from McGill’s Dept. of Biology. “The cells in an elephant grow more than 100 times more slowly than those of a mouse.”

“The discovery of ecosystem-level scaling laws is particularly exciting,” added co-author Michel Loreau, adjunct professor in McGill’s Biology Dept. and currently at the Centre national de recherché scientifique (CNRS) in France. “Their most intriguing aspect is that they recur across levels of organization, from individuals to ecosystems, and yet ecosystem-level scaling laws cannot be explained by their individual-level counterparts. It seems that some basic processes reemerge across levels of organization, but we do not yet fully understand which ones and why.”


Ecosystems still feel the pain of ancient extinctions

The more researchers study ecosystems, the more we learn that an ecosystem behaves, in many ways, just like a living organism: thousands of years after human hunters wiped out big land animals like giant ground sloths, the ecosystems they lived in are still suffering from the effects, much like a body suffers from past trauma.

The giant sloth, imagined in happier days. Image: Jaime Chirinos/SPL

The giant sloth, imagined in happier days. Image: Jaime Chirinos/SPL

Humans wiping out species (directly through hunting or indirectly through habitat destruction) is not really a new thing. Early human hunters have posed a stress on environments for thousands if not tens of thousands of years, because they were so successful and the prey didn’t have enough time to adapt.

Most ecosystems rely on big animals to supply them with nutrients (read: dung fertilizing).

“If you remove the big animals from an ecosystem, you pretty much stop nutrients moving,” says Chris Doughty of the University of Oxford.

In order to understand the impact of this extinction, Doughty and his colleagues studied the distribution of phosphorous – a nutrient that plants need to grow; he analyzed the Amazon basin in South America, an area which was once the home of fantastically large animals, such as elephant-like gomphotheres and giant ground sloths.

Unfortunately for these spectacular animals though, some 12.500 years ago, humans moved to South America, and shortly after this, these animals went extinct due to extensive hunting and climate change. Today, the Amazon basin is home to a huge biodiversity, but there are no more truly big animals – and their extinction still has a massive effect on the distribution of phosphorous throughout the basin.

Using the relationship between animal size and phosphorous distribution, Doughty estimated how much phosphorus South America’s larger extinct animals would have transported 15,000 years ago. His model concluded that megafauna would have spread nutrients 50 times faster than today’s fauna. This happens because big animals carry more food around in their bellies and they also travel more searching for food. It’s just like blood vessels in the body:

When you get rid of big animals, it’s like severing the nutrient arteries.”, says Doughty. He thinks the same thing happened in North America, Europe and Australia, where most big animals have also been wiped out. “The idea that herbivores redistribute nutrients is not new, but the scale of this thinking is much, much bigger,” says Tim Baker at the University of Leeds in the UK.

If his model is correct, than it’s quite safe to assume that the Amazon is still recovering from this drastic event which severely altered the circuit of nutrients. With large herbivores gone from the area, it’s up to the humans to take their role – but we’re doing the complete opposite of what they’re doing.

amazon basin

“These megafauna would disperse nutrients, whereas humans concentrate them,” says Doughty. We spread fertiliser on small plots of productive farmland, and keep large animals like cows fenced rather than letting them roam freely. “There are probably more nutrients because of people, but they are very poorly distributed.”

New study estimates 1 million marine species – one third still unknown

The world’s oceans are teeming with life, a new census estimating almost 1 million species out there; but marine life is declining, with the main causes being overfishing, ocean acidification and coastal damage.

Avoiding a crisis

The new numbers are just estimates, but they are much lower than previous studies, which put the number of species at around 10 million; even still, the species-by-species count is extremely important, enabling researchers to better understand biodiversity and the complex relationships between species in the same ecosystem and even between different ecosystems – something crucial for biodiversity conservation.

“It’s the best job ever of tallying everything we know – and what we don’t know – about life in the oceans today,” Palumbi said. “It’s the first time anyone’s done this kind of dirty work that’s so important with the world’s oceans facing a biodiversity crisis.”

Some scientists believe this kind of crisis is imminent, others are more reserved, believing the damage is not irreparable, but all of then agree on one thing: mankind is making a bigger and bigger mark on oceanic wildlife. The first thing we must do in order to minimize our impact is to understand how it all works.

“You can only love something if you know it,” said Ward Appeltans, a marine biologist at the Intergovernmental Oceanographic Commission of UNESCO in Oostende, Belgium. “We will not save the world with this result, but we may start understanding it better.”

Unknown species

The good news is researchers are quite optimistic about our chances to identify all marine species.

“It may not be mission impossible to describe all the marine species in the ocean,” Appeltans said. “We are describing 2,000 new marine species every year. If we can keep that momentum, we can start knowing exactly what’s living on our planet.”

Quick math says that if there are 1.000.000 species in the ocean, and 333.000 are still undescovered, at a rate of 2.000 per year, it would take some 166 years – but that’s assuming the rate doesn’t go down, which is quite unlikely.

Previous estimates regarding the number of species in the ocean relied mostly on extrapolations based on rates of previous discoveries or numbers of unknown species in sample collections – a method which led to estimates ranging from 300.000 to 10 million. In order to get to something more accurate, Appeltans worked with 120 of the world’s leading experts on specific groups of marine environments. He relied on their taxonomic knowledge, and then asked them to make educated guesses about the numbers of unknown species in their fields. He then summed it up and ran the numbers through a statistical model which also took into consideration the changes in rates of discovery over time.

Overall, he analyzed some 400.000 known species, and using the technique described above, he calculated 482.000 to 741.000 species are yet to be discovered. Experts predicted that most of them would be crustaceans, mollusks, phytoplankton and other small organisms, but also 2-8 species of whales and dolphins, 10 species of sea snakes, and other reptiles.

“The question of how many species there are is such a fundamental one and it’s a huge embarrassment that we don’t have the answer,” said Stuart Pimm, a conservation biologist at Duke University in Durham, North Carolina. “In a compelling way, this paper has come up with a fairly credible number for how much we know and don’t know.”

It’s not the exact number that’s important, but rather what it means. It could help us understand if we’re protecting the areas we should be, or if we’re ignoring some areas we really shouldn’t. Marine conservation and environmental protection are extremely serious issues which could benefit from this research.

“We know we’re losing biodiversity at a rate that is 1,000 times faster than we should be, and if we’re going to stop that hemorrhaging of species, we have to know what the species are and most important, where they are,” Pimm said. “This is a vital first step in making decisions about where to act.”

You can find the entire database on marinespecies.org

The research was published in “Current biology

Earth took 10 million years to recover from biggest extinction

Some 250 million years ago, life on Earth passed through its toughest time so far, as 96% of all marine species and over three quarters of land vertebrates went extinct. According to British researchers, the mass extinction was so severe that it took life 10 million years to recover.

With less than 10 percent of plants and animals surviving and a huge number of biological niches left unfilled, a quick bounce back could seem likely, but according to Dr Zhong-Qiang Chen, from the China University of Geosciences in Wuhan, and Professor Michael Benton from the University of Bristol, that’s not really the case; two reasons stood in the way of life: the sheer intensity of the crisis, and continuing grim conditions on Earth after the first wave of extinction.

The Permian-Triassic extinction took place at the end of the Permian period, and in those times, living on our planet was hellish: global warming, ocean acidification and ocean anoxia (lack of oxygen) all worked together to wipe out the biggest part of life on Earth.

“It is hard to imagine how so much of life could have been killed, but there is no doubt from some of the fantastic rock sections in China and elsewhere round the world that this was the biggest crisis ever faced by life,” Dr Chen said.

Current research of the conditions showed that things didn’t become pink after that – six million years after the main event conditions didn’t change significantly with repeated carbon and oxygen crises, warming and other ill effects. Some groups of animals on the sea and land did recover quickly and began to rebuild their ecosystems, but they suffered further setbacks.

“Life seemed to be getting back to normal when another crisis hit and set it back again,” Professor Benton, Professor of Vertebrate Palaeontology at the University of Bristol, said. “The carbon crises were repeated many times, and then finally conditions became normal again after five million years or so.”

However, after the environmental crisis ceased, more complex ecosystems emerged, including ancestral crabs and lobsters, as well as the first marine reptiles, paving the way for modern marine ecosystems.

“We often see mass extinctions as entirely negative but in this most devastating case, life did recover, after many millions of years, and new groups emerged. The event had re-set evolution. However, the causes of the killing – global warming, acid rain, ocean acidification – sound eerily familiar to us today. Perhaps we can learn something from these ancient events,” Professor Benton added.


Seagrass on ocean coasts can store twice as much carbon as tropical rainforests, yet face destruction

A new research from a team of international marine geoscientists has found that seagrass meadows, found in coastal regions, can store up to twice as much carbon as temperate or tropical forests. The scientists involved in the study, thus, believe that seagrasses can potentially become a viable solution to climate change, if scaled and preserved through out the world.


Dense seagrass meadows in Florida's Coastal Everglades LTER site.(c) Florida Coastal Everglades LTER Site

Data suggests that coastal seagrass beds store up to 83,000 metric tons of carbon per square kilometer, mostly in the soils beneath them. Some seagrass beds have been found to store carbon for thousands of years in the roots and soil beneath them. Actually, seagrass beds store 90% of their carbon in the soil–and continue to build on it for centuries.

The research also estimates that, although seagrass meadows occupy less than 0.2 percent of the world’s oceans, they are responsible for more than 10 percent of all carbon buried annually in the sea.

“Seagrasses only take up a small percentage of global coastal area, but this assessment shows that they’re a dynamic ecosystem for carbon transformation,” said James Fourqurean, the lead author of the paper and a scientist at Florida International University and the National Science Foundation’s (NSF) Florida Coastal Everglades Long-Term Ecological Research (LTER) site.

Despite this, however, seagrass meadows are among the world’s most threatened ecosystems. Currently, some 29% of the world’s historic sea grass meadows have been destroyed, preponderantly caused by water pollution and dredging. It’s estimated some 1.5% of the world’s seagrass meadows are lost every year.

The current study explicitly shows how important, really, are seagrass ecosystems to the Earth’s climate and why preservation and rehabilitation efforts are required. Destruction of seagrass meadows can potentially emit up to 25 percent as much carbon as those from terrestrial deforestation, the researchers claim in the study recently published in the journal Nature Geoscience.

“One remarkable thing about seagrass meadows is that, if restored, they can effectively and rapidly sequester carbon and reestablish lost carbon sinks,” said paper co-author Karen McGlathery, a scientist at the University of Virginia and NSF’s Virginia Coast Reserve LTER site.

Besides storing carbon, seagrass beds are beneficial to the ecosystem also by filtering sediment from the oceans; protecting coastlines against floods and storms; and serving as habitats for fish and other marine life.

The research was led by Fourqurean in partnership with scientists at the Spanish High Council for Scientific Investigation, the Oceans Institute at the University of Western Australia, Bangor University in the United Kingdom, the University of Southern Denmark, the Hellenic Center for Marine Research in Greece, Aarhus University in Denmark and the University of Virginia.

source: physorg