Biodiversity Soil and Fertilizer

Life in the Ground ~ Soil Biota

Over the next few posts, I’ll be trying to catch up on the many articles I’ve collected about soil.

Samples were harvested at two time points in July and October 2019 at two long-term warming experiments, SWaN and PH, at the Harvard Forest long-term ecological research station, which had been established for 13 and 28 years, respectively. Credit: Global Change Biology (2022).

How are soil microbes affected by climate change?

The largest terrestrial carbon sink on Earth is the planet’s soil. One of the big fears is that a warming planet will liberate significant portions of the soil’s carbon, turning it into carbon dioxide (CO2) gas, and so further accelerate the pace of planetary warming. A key player in this story is the microbe, the predominant form of life on Earth, and which can either turn organic carbon—the fallen leaves, rotting tree stumps, dead roots and other organic matter—into soil, or release it into the atmosphere as CO2. Now, an international team of researchers led by the University of Massachusetts Amherst has helped to untangle one of the knottiest questions involving soil microbes and climate change: what effect does a warming planet have on the microbes’ carbon cycling? The answer is surprising: increased temperature decreases the rate at which soil microbes respire CO2—but only in the summer. During the rest of the year, microbial activity remains largely historically consistent.

But there’s a catch to this seemingly happy story. Soil microbes are releasing less CO2 in the summer because they’re starving. And they’re starving because long-term warming is threatening the viability of deciduous trees, on whose dead leaves the microbes depend. “One of the major outcomes of our study,” says Kristen DeAngelis, professor of microbiology at the University of Massachusetts Amherst and senior author of the study, published in the journal Global Change Biology, “is that all those autumn leaves mitigate the negative effects of global warming on soil microbes.” For now. But fewer dead leaves means less food for the microbes and seems to be leading to a reduction in microbial biomass during the summer.

Modelling bacterial diversity of soils

Credit: Pixabay/CC0 Public Domain

A new set of quantitative models that incorporates pH into the metabolic theory of ecology (MTE) has been developed by an international team that includes Penn State assistant professor of plant science Francisco Dini-Andreote. The work is included in a paper published by the Proceedings of the National Academy of Sciences. In general terms, the metabolic theory of ecology links rates of organism diversification (i.e., the metabolic rate of an organism) with the organisms’ body size and body temperature. “Soils are the most complex and biodiverse ecosystems on Earth,” said Dini-Andreote, a member of Penn State’s Microbiome Center. “In soils, microbial diversity plays indispensable roles in the anabolic and catabolic cycles of carbon, nitrogen and sulfur, without which the diversity of life forms—including plants, animals and other microbes—that evolved on our planet would not have been possible. In addition, advancing our ability to predict patterns of soil biodiversity is critical to better understanding how climate change will affect soil functioning and how soil microbes will respond to shifts in temperature and precipitation regimes.”

It isn’t the picky eaters that drive soil microbial metabolism

Soil sample from the Washington State University field site in Prosser, Washington. Credit: Andrea Starr, Pacific Northwest National Laboratory

Interactions among microorganisms in soil lead to the release of nutrients derived from complex organic matter in that soil. This community metabolism creates food for both microbes and plants. However, scientists don’t fully understand the specific nature of many of these interactions. For example, scientists want to know why some microbes are more successful than others and what roles individual members play in their communities. To find out, researchers from Pacific Northwest National Laboratory, Iowa State University, University of Nebraska–Lincoln, and Argonne National Laboratory studied a model microbial community fed with a complex source of carbon and nitrogen commonly found in soils—chitin.

Their findings, published in the journal mSystems, show that certain microbes drive specific steps of the chitin breakdown process, but the most abundant microbes are not necessarily the most important. The model microbial community used in this study included eight soil bacteria—some chitin degraders and some non-degraders. The researchers observed that the species organized into distinct roles when it was time to break down the chitin. Intriguingly, the most abundant members of the model community were not those that were able to break down chitin itself, but rather those that were able to take full advantage of interactions with other community members to grow using chitin breakdown products. The study answers important questions about how complex carbon and nutrient sources are metabolized by interacting microorganisms to support plant and microbial growth in soil ecosystems.

Microbes could be used by farmers as natural fertilizer for poor soil

A hammer and chisel were required to collect samples from the terrain where Barbacenia macranta lives, in this case, exposed rock. Credit: Rafael Soares Correa de Souza/GCCRC

A study published in The ISME Journal identified 522 genomes of archaea and bacteria associated with the roots and soil of two plant species native to the Brazilian montane savanna ecoregion known as campos rupestres (“rocky meadows”). Hundreds of microorganisms hitherto unknown to science were identified, showing that the ecoregion is a biodiversity hotspot and that many new organisms have yet to be described and classified in Brazil.

The discovery could potentially be a basis for the development of biological substitutes for the chemical fertilizers used by farmers, especially those containing phosphorus. “Phosphorus is normally present in the soil, but not always in a form that plants can use. Most of the microorganisms we found make phosphorus soluble so that plants can absorb it,” said Antônio Camargo, first author of the article.

Fungi and bacteria are binging on burned soil

Signs of microbial life in the Holy Fire burn scar. Credit: Sydney Glassman/UCR

UC Riverside researchers have identified tiny organisms that not only survive but thrive during the first year after a wildfire. The findings could help bring land back to life after fires that are increasing in both size and severity. The Holy Fire burned more than 23,000 acres across Orange and Riverside counties in 2018. Wanting to understand how the blaze affected bacteria and fungi over time, UCR mycologist Sydney Glassman led a team of researchers into the burn scar. “When we first came into fire territory, there was ash up to my shins. It was a very severe fire,” Glassman said.

The researchers visited the scar nine times over the course of the next year, comparing the charred earth with samples from nearby, unburned soil. Their findings, now published in the journal Molecular Ecology, show that the overall mass of microbes dropped between 50 and 80% after the fire, and did not recover during that first year. However, some things lived. 

UCR researcher sampling soil in the Holy Fire burn scar. Credit: Sydney Glassman/UCR.

It wasn’t just one type of bacteria or fungi that survived. Rather, it was a parade of microbes that took turns dominating the burned soil in that first post-fire year. “There were interesting, distinct shifts in the microbes over time. As one species went down, another came up,” Glassman said.

Certain microbes called methanotrophs regulate the breakdown of methane, a greenhouse gas. Fabiola Pulido-Chavez, UCR plant pathology Ph.D. candidate and first author of the study, noticed that genes involved in methane metabolism doubled in post-fire microbes. “This exciting finding suggests post-fire microbes can “eat” methane to gain carbon and energy, and can potentially help us reduce greenhouses gases,” Pulido-Chavez said.

What the researchers saw in the soil bears some resemblance to the human body’s response to a major stress. What is now being learned about post-fire microbe behavior could change older theories about plant behavior, since microbes were not factored into them. “To me, this is exciting, as microbes have long been overlooked, yet they are essential for ecosystem health,” Pulido-Chavez said.

One open question that remains is whether adaptations that plants and microbes have developed in response to wildfires will adapt again to megafires or recurrent fires. Whereas there might have been a period of several decades before a plot of land burned more than once, it is increasingly common for the same soil to burn again in fewer than 10 years.


Plants in History

One of my favorite categories of garden-related science stories is one I call “eye-candy, oddities & miscellany”. It includes articles that celebrate the beauty of nature and our gardens, stories that make me say “wow” – sometimes out loud, and reports of general weirdness. I last posted something on this category in mid-January. Since then, I’ve accumulated so many such stories that I’m breaking the category into three. Let’s start with historical notes relating to plants.

A 2000-year old loaf of bread. Image courtesy of Museo Archeologico Nazionale di Napoli.

2000-Year old Roman bread recipe

While many occupied their COVID lockdown time learning to bake bread, how about a truly historical recipe? Mihai Andrei, editor in chief at ZME Science shares a sourdough recipe from Pompei and how it came to be rediscovered thanks to archaeology and chemistry research.

Close-up of carving on wood, Patrai, Greece (De Agostini via Getty Images)

Drinking culture

In Salon, staff writer Troy Farah interviews UBC philosophy professor Edward Slingerland about his provocative theory and the book it inspired. In his 2021 book, “Drunk: How We Sipped, Danced, and Stumbled Our Way to Civilization,” Slingerland lays out the case that alcohol may have even been the impetus for humans developing agriculture and complex societies. Slingerland found evidence that, as he writes, “various forms of alcohol were not merely a by-product of the invention of agriculture, but actually a motivation for it — that the first farmers were driven by a desire for beer, not bread.”

When asked for examples, Slingerland notes the following. “When I started doing the research, I encountered this movement in archaeology that I think is gaining adherence and seems quite plausible. That’s called the Beer Before Bread hypothesis. So 13,000 years ago or so, we’re coming together, building these monumental religious sites and feasting. And feasting involved eating meat and other kind of high value items, but also drinking beer. Sites like Gobekli Tepe, [the world’s oldest surviving permanent human settlement], we don’t have direct chemical evidence, but we have these big vats. They were drinking some kind of liquid. And we know from other sites in the area, they were making beer at this time. In some cases beer, probably laced with psychedelics. So in that respect, the desire to get intoxicated actually directly led to civilization. It’s what motivated hunter gatherers to start cultivating crops and settling down. And you see this pattern around the world, not just in the Fertile Crescent but also Mideast, which is now the modern Turkey area, where agriculture first got started.”

Heriot-Watt’s International Centre for Brewing and Distilling is using 200-year-old barley in a project with Holyrood Distillery in Edinburgh. Credit: Holyrood Distillery

200-year-old barley for modern whisky

Heriot-Watt University’s Dr Calum Holmes is working to develop new whiskeys using old strains of barley. Experts from Heriot-Watt’s International Centre for Brewing and Distilling (ICBD) are working with Holyrood Distillery in Edinburgh to find out whether old species of barley could create distinctive new whiskies. Over the next six years, they’ll test at least eight heritage barley varieties and provide the scientific evidence needed to classify the flavours and aromas they bring to a dram. “There’s hope that using these heritage varieties of barley might allow for recovery of favourable aroma characteristics.”, says Dr. Holmes. 200-year-old Chevallier is one of the varieties they’ll be distilling. It was the most popular barley in Britain for 100 years but fell out of favour when tax rules changed. They’ll also test Hana, which was originally grown in Czech Moravia and was used to make the first blond Pilsner lager in 1842. Golden Promise is from the 1960s and grows predominantly on the east coast of Britain, from Angus down to Northumberland. It is best known as the barely behind the iconic Macallan bottlings from the sixties. The team hopes that the research will create new single malts for Holyrood Distillery and increase knowledge and awareness about the positive traits of heritage barleys. 

“The Houses of Parliament, Sunset,” by Claude Monet (1913). Image credit: Active Museum/Active Art/Alamy Stock Photo.

Hazy impressionist landscapes

Impressionist artists like Claude Monet and Joseph Mallord William (J. M. W.) Turner are famous for their hazy, dreamlike paintings. However, a new study finds that what these European painters were really depicting in their works wasn’t a figment of their imagination, but an environmental disaster: air pollution. Scientists examined approximately 100 artworks by the two impressionist painters, who dominated the art scene between the mid-18th and early 20th centuries, during the Industrial Revolution. The team discovered that what some art enthusiasts had long believed was Monet and Turner’s style of painting was actually them “capturing changes in the optical environment” that were associated with a decrease in air quality as coal-burning factories began dotting European cities and spewing pollutants into the air, according to the study, published in the journal Proceedings of the National Academy of Sciences.

The son of study first author Zhuo Feng, of Yunnan University in Kunming, China collecting a leaf of Bauhinia that shows signs of symmetrical insect-feeding damage. Image credit: Zhuo Feng (CC BY-SA).

Plants ‘slept’ with curled leaves 250 million years ago

Each night at sunset, a handful of plants “fall asleep.” Species as diverse as legumes and daisies curl up their leaves and petals for the evening and do not unfurl until morning. Now, a new study suggests that plants may have been folding their leaves at night for more than 250 million years. By tracking the unique bite marks that insects inflict only upon folded leaves, the authors determined that one extinct group of plants were likely nyctinastic — the scientific term for plants curling up in response to darkness.

Evidence of insect feeding damage on the leaf of the now extinct Gigantopterid. Image credit: Current Biology/Feng et al. (CC BY-SA).

“Since it is impossible to tell whether a folded leaf found in the fossil record was closed because it experienced sleeping behavior or because it shriveled and bent after death, we looked for insect damage patterns that are unique to plants with nyctinastic behavior,” study co-author Stephen McLoughlin, curator of Paleozoic and Mesozoic plants fossil collections at the Swedish Museum of Natural History in Stockholm, said in a statement(opens in new tab). “We found one group of fossil plants that reveals a very ancient origin for this behavioral strategy.”

After examining hundreds of specimens and photographs of gigantopterid fossils, the authors discovered symmetrical holes indicating that the leaves of these prehistoric plants were mature and folded when they were bitten. The results, published in the journal Current Biology, provide the strongest evidence to date of nyctinasty in ancient plant species.

Biodiversity Citizen Science Conservation Miscellany Pollinators, Molluscs and Other Invertebrates

December 2022: Pollinator & Invertebrate Round-up

Image courtesy of Empress of Dirt

‘Bees get all the credit’: slugs and snails among 2023 Chelsea flower show stars: Stag beetles and hornets will be among the stars of Chelsea flower show next year as horticulturalists encourage people to welcome invertebrates into the garden. Bumblebees and butterflies tend to get a lot of press, but in a 2023 garden sponsored by the Royal Entomological Society, less glamorous creepy-crawlies will take centre stage. The garden may startle those used to more pristine spaces, as it will feature rotting wood and leaves as habitat for beetles and other insects, but it will still include a vast array of native and non-native flowering plants, which will be there to encourage pollinators. It will highlight how pollination, food security and preventing vector-borne diseases are critical to our survival in a changing world and that insect conservation is often undervalued compared with mammal and bird conservation. [Editor’s note: this article includes tips on insect-friendly gardening.]

(A) Overall view of the experimental setup during training. The wooden box was covered by a transparent cover, which allowed observing the behavior of the bees accessing the inner compartments. After passing the first inner compartment, the focal bee faced a training stimulus placed in the middle of the back wall. An Eppendorf tip delivered sucrose solution in the middle of the image. (B) Overall view of the experimental setup during a test. After passing the first inner compartment, the focal bee faced two lateral walls displaying the same test alternative on each side. The test stimuli were novel to the trained bee, i.e. they were never experienced during the training. No reward was provided during the test. The first choice and the cumulative choices performed during 40 s were recorded. (C) Examples of stimuli used in the first and second experiment. (D) Stimuli used in the third experiment. (E) Examples of stimuli used in the fourth experiment. Credit: Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2203584119

Honeybees use a ‘mental number line’ to keep track of things: A small team of researchers with members from the University of Toulouse, the University of Lausanne and the University of Padova has found evidence that honeybees have a mental number line in their tiny brains. In their paper published in Proceedings of the National Academy of Sciences, the group describes experiments they conducted with captive honeybees. Prior research has suggested that in to addition humans, baby chickens possess what scientists call a mental number line. Numbers of things are represented in the brain and are processed in a left-to-right direction. For example, when most people are asked to sort piles of grapes by the number, most do so from left to right, with the smallest pile on the left. In this new effort, the researchers wondered whether honeybees might also use a mental number line to keep track of things. To find out, they conducted a two-stage experiment.

Credit: N. Gamonal, Didde Sørensen

Following insect ‘footprints’ to improve crop resilience and monitor pollinator biodiversity: Bees and other insects leave behind tiny “footprints” of environmental DNA on plants each time they visit, giving researchers a way of tracking where insects have been, and offering clues on how to help them flourish. A team of researchers, including the Wellcome Sanger Institute and led by the University of Copenhagen, have used these DNA footprints as a non-invasive way to collect information on insect biodiversity, giving new insight into how to boost pollination and protect insect biodiversity and crops against threats such as climate change. The new study, published in Environmental DNA, is the first time DNA footprints have been used alongside visual observations to track the kind of insect visitors to crops, helping to see if there are any pests and informing new ways to encourage beneficial insects. Didde Hedegaard Sørensen, laboratory technician and an author from the University of Copenhagen, Denmark says, “The exciting thing about this study is that it can have an immediate, real-world impact on agricultural systems. Our results can assist farmers in managing their crops against the rising threats of reduced pollinators. Environmental DNA can be used to investigate the biodiversity in agricultural landscapes beyond apple orchards, making it a fast and non-invasive way to gain more knowledge about the world around us.”

AI rendering bees and electricity. Credit: Ellard Hunting

Insects contribute to atmospheric electricity: By measuring the electrical fields near swarming honeybees, researchers have discovered that insects can produce as much atmospheric electric charge as a thunderstorm cloud. This type of electricity helps shape weather events, aids insects in finding food, and lifts spiders up in the air to migrate over large distances. The research, appearing in the journal iScience, demonstrates that living things can have an impact on atmospheric electricity.

Credit: CC0 Public Domain

California county sees highest number of monarch butterflies in more than 20 years: There’s some hope fluttering around San Luis Obispo County this holiday season. It comes in the form of an iconic orange-and-black striped butterfly that makes tall eucalyptus or Monterey cypress trees its home up and down the coast. More than 129,000 western monarch butterflies were counted in the county by Xerces Society for Invertebrate Conservation employees and volunteers in November, according to preliminary data shared by local volunteer coordinator Jessica Griffiths. That’s the most counted in San Luis Obispo County in more than 20 years—in 1998 there were about 182,000 counted, according to the Xerces Society’s data. The numbers are giving some researchers hope that the western monarch butterfly population could be rebounding from devastatingly low numbers a few years ago that left some worrying the insect was on the verge of extinction.

Arizona’s state butterfly, the two-tailed swallowtail butterfly, can be found at Tucson-area botanical gardens. Credit: Jeff Oliver/University Libraries

Botanical gardens are ‘hot spots’ for butterflies amid climate change: Despite their relatively small footprint in urban areas, botanical gardens are important hotspots for butterfly biodiversity in the arid Southwest, according to a new study by University of Arizona scientists published in the journal Insects. Using more than 10,500 community science observations spanning roughly 20 years, researchers compared butterfly species richness and diversity in botanical gardens versus in the gardens’ surrounding metropolitan areas. The study focused on five large, urban cities in the Southwest, including Tucson and Phoenix in Arizona; Palm Desert, California; Albuquerque, New Mexico; and El Paso, Texas. Each city averages less than 11 inches of precipitation annually and, with the exception of Palm Desert, each has a population over 500,000 residents. While botanical gardens represent less than 1% of metropolitan landscapes—between 0.002–0.22% on average—these urban green areas have disproportionately high butterfly species richness and diversity compared to the much larger surrounding city areas. In fact, species richness in these gardens scored in the 86th percentile or above, according to the study.

Screen grab from YouTube video.

These bumblebees like playing and it’s the sweetest thing: Playing is an important behavior in humans — it helps us learn new skills, improve control over our bodies, and also helps with bonding. In other mammals, play has also been documented as an important behavior — but in insects, playing has been far less studied. For Lars Chittka, a behavioral ecologist at Queen Mary University of London (QMUL), peering into the minds of bees has been a long-term interest. Chittka recently published a book called the Mind of a Bee, where he highlights many of the remarkable findings about the intellect and behavior of bees. But this new study came almost by accident. Chittka and his team were looking at how bumblebees learn complex behaviors. In a scientific setup, bees had to move wooden balls, and if they moved them to the right place, they got a sweet reward. But the researchers started noticing how some bees would just push the balls around even without any reward. This was puzzling, so the researchers started looking at this in more detail. The study followed 45 bumblebees in an arena who chose between walking through an unobstructed, clear path and reaching a feeding area and deviating from this path to fiddle with wooden balls. There was no advantage to rolling the balls, and there is no analogue behavior in the wild that would prompt bees to roll the balls. Still, all individual bees rolled the balls between 1 and 117 times — a strikingly large number that strongly suggests the bees found pleasure in this activity. Note article includes 1:30 video from the BBC that shows the bees playing with wooden balls. (See also: First-ever study shows bumble bees ‘play’)

Screen grab from YouTube video showing leafhopper baby “Mildred” in her new dress.

True Facts: Leafhoppers and Friends

This 5-minute video features stunning macro shots of tiny leafhopper  babies with scientifically accurate and hysterically funny commentary. You’ll never look at leafhoppers quite the same way again! Thanks to reader Carol English for sharing.