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Unraveling sex determination in Bursaphelenchus nematodes: A path towards pest control

by Meiji University

Unraveling sex determination in Bursaphelenchus nematodes: A path towards pest control
Scientists discover that sex determination in nematodes of the genus Bursaphelenchus can be attributed to random events rather than well-known mechanisms such as genetic or environmental sex determination. Credit: Associate Professor Ryoji Shinya, Meiji University

The sex and sexual characteristics constitute key aspects of an organism’s life and are determined by a biological process known as sex determination. These ever-evolving mechanisms are broadly classified based on the type of “switch” that triggers them. Genetic sex determination is dependent on sex chromosomes, such as the X and Y chromosomes in human beings, whereas environmental sex determination depends on factors like temperature and the local ratio between males and females. Although most sex determination mechanisms are genetic or environmental, a third type of sex determination, which depends on completely random factors, also exists. This, however, has not been explored completely.


The sex determination mechanism of Caenorhabditis elegans, a species of nematode, or our common garden-variety roundworm, is one of the best understood aspects of its biology. In its case, embryos with two X chromosomes, or the XX embryos, develop into hermaphrodites, while the XO embryos, which have one sex chromosome—the X chromosome—develop into males. Several species of nematodes have a sex determination mechanism similar to that of C. elegans. Interestingly, however, some nematode species also rely on the XX/XY system for sex determination, with both X and Y types of sex chromosomes, as well on environmental factors. Unfortunately, the mechanisms that cause this variance in sex-determination between nematode species have remained a mystery thus far.

Recently, a group of researchers led by Associate Professor Ryoji Shinya from Meiji University, Japan, Professor Paul Sternberg from the California Institute of Technology, U.S., and Associate Professor Taisei Kikuchi from the University of Miyazaki, Japan, conducted a study to understand sex determination in two nematode species—Bursaphelenchus xylophilus and Bursaphelenchus okinawaensis. Dr. Shinya’s team have long been engaged with nematode research. In this new study, they conducted a sex-specific genome-wide comparative analysis to determine the initial trigger of sex determination in the two Bursaphelenchus species, and genetic screening to determine the genetic cascade that followed the trigger.

In their study published in Nature Communications, the researchers report that there is no difference in the number of chromosomes, or the genome, between males and females in B. xylophilus and between males and hermaphrodites in B. okinawaensis. This suggests that these sexes in both nematode species have identical genomes and no sex chromosomes. Thus, sex determination in these species must be through non-genetic mechanisms.Play


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PlayCredit: Meiji University, Tokyo, Japan

To explore this further, the team conducted an analysis to find out if environmental factors such as temperature, nutrient availability, and population density influenced sex determination in these organisms. They observed that these factors had a minimal effect on sex determination in the larvae of these species, and that none of the larvae turned into males.

Considering that the offspring produced through self-fertilization in B. okinawaensis are essentially isogenic clones, it is clear that genetic differences are not required for sex determination in B. okinawaensis. In addition, even under fixed environmental conditions, genetically identical individuals of B. okinawaensis differentiate into hermaphrodites and males. The team suggests that the sex of B. okinawaensis nematodes is mainly determined by stochastic expression of an unknown trigger gene and/or developmental noise. In other words, sex differentiation occurs as a result of random events during development.

The team also compared the orthologs, i.e., genes related by common descent, of similar sequences in C. elegans, B. xylophilus, and B. okinawaensis. They found that only downstream genes in these three nematodes were conserved, indicating that the Bursaphelenchus genus has a different sex determination trigger than does C. elegans. In addition, they conducted genetic analyses and identified one major sex determining locus in B. okinawaensis, known as Bok-tra-1a. Using bioinformatics and RNA-sequencing, they observed a conservation of putative targets in this regulating gene, further supporting the findings that indicated the conservation of downstream functions. This implies that nematode sex differentiation might have evolved from this downstream regulator.

“Our discovery of a striking new mode of sex determination in the nematode phylum might help not only with lab studies of parasitic nematodes, but also contribute to population engineering,” observed an excited Dr. Shinya.

Indicating the importance of these findings in pest control, Dr. Shinya says, “Damage caused by plant-parasitic nematodes is estimated at 80 billion USD per year. Conventional nematicides are harmful for the environment. Understanding the sex determination mechanisms of plant parasitic nematodes can help in developing sterile strains that are not parasitic but may help reduce nematode populations in a safe and sustainable way.”

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Parasitic worms reveal new insights into the evolution of sex and sex chromosomes

More information: Ryoji Shinya et al, Possible stochastic sex determination in Bursaphelenchus nematodes, Nature Communications (2022). DOI: 10.1038/s41467-022-30173-2

Journal information: Nature Communications 

Provided by Meiji University

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Francis to retire after 45 years at Nebraska Charles “Chuck” Francis, University of Nebraska–Lincoln professor in agronomy and horticulture, will retire June 30 after a 45-year career at Nebraska.

GPPN Followers:

I have attached the article on Chuck Francis because he has had an extensive international career and I am sure that some of you readers of the GPPN have had him visit your country, he may have been your mentor at the University of Nebraska or you have met him somewhere..

E.A. “Short” Heinrichs

IAPPS Secretary General and Membership Manager


Francis to retire after 45 years at Nebraska Charles “Chuck” Francis, University of Nebraska–Lincoln professor in agronomy and horticulture, will retire June 30 after a 45-year career at Nebraska. Charles “Chuck” Francis

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Science News

from research organizations

Dragonflies use vision, subtle wing control to straighten up and fly right

Date:May 13, 2022Source:Cornell UniversitySummary:Researchers have untangled the intricate physics and neural controls that enable dragonflies to right themselves while they’re falling.Share:


With their stretched bodies, immense wingspan and iridescent coloring, dragonflies are a unique sight. But their originality doesn’t end with their looks: As one of the oldest insect species on the planet, they are an early innovator of aerial flight.

Now, a group led by Jane Wang, professor of mechanical engineering and physics in the College of Arts and Sciences, has untangled the intricate physics and neural controls that enable dragonflies to right themselves while they’re falling.

The research reveals a chain of mechanisms that begins with the dragonfly’s eyes — all five of them — and continues through its muscles and wing pitch.

The team’s paper, “Recovery Mechanisms in the Dragonfly Righting Reflex,” published May 12 in Science. Wang co-authored the paper with James Melfi, Ph.D. ’15, and Anthony Leonardo of Howard Hughes Medical Institute (HHMI) in Ashburn, Virginia.

For two decades, Wang has been using complex mathematical modeling to understand the mechanics of insect flight. For Wang, physics is just as important as genetics in explaining the evolution of living organisms.

“Insects are the most abundant species and were the first to discover aerial flight. And dragonflies are some of the most ancient insects,” Wang said. “Trying to look at how they right themselves in air would give us insight about both the origin of flight and how animals evolved neuro-circuitries for balancing in air and navigating through space.”

The project began several years ago when Wang was a visiting scientist at HHMI’s Janelia Research Campus, where her collaborator Leonardo was 3D-tracking dragonflies in a large arena. Wang was inspired to scrutinize them more closely.

“When we looked at their flight behavior, we were simultaneously in awe and frustrated,” she said. “The trajectories are complex and unpredictable. Dragonflies constantly make maneuvers, without following any obvious direction. It’s mysterious.”

To study these flight dynamics and the internal algorithms that govern them, Wang and Melfi designed a controlled-behavioral experiment in which a dragonfly would be dropped upside down from a magnetic tether — a premise not unlike the famous falling cat experiments from the 1800s that showed how certain “hardwired reflexes” resulted in the felines landing on their feet.

Wang and Melfi found that by releasing a dragonfly carefully without leg contact, the insect’sconfounding maneuvers actually followed the same pattern of motion, which the researchers were able to capture with three high-speed video cameras filming at 4,000 frames per second. Markers were put on the dragonfly’s wings and body, and the motions were reconstructed via 3D-tracking software.

Then came the most challenging part: trying to make sense of the movements. The researchers had to consider numerous factors — from the unsteady aerodynamics of wing and air interactions to the way a dragonfly’s body responds to its wings flapping. There’s also that persnickety force that all earthly beings must eventually contend with: gravity.

Wang and Melfi were able to create a computational model that successfully simulated the dragonfly’s aerobatics. But one key question lingered: How do dragonflies know they are falling, so that they can correct their trajectory?

Wang realized that, unlike humans who have an inertial sense, dragonflies could rely on their two visual systems — a pair of large compound eyes, and three simple eyes called ocelli — to gauge their uprightness.

She tested her theory by blocking a dragonfly’s eyes with paint and repeating the experiment. This time, the dragonfly had much more difficulty recovering midflight.

“These experiments suggest that vision is the first and dominant pathway to initiate the dragonfly’s righting reflex,” Wang said.

That visual cue triggers a series of reflexes that sends neural signals to the dragonfly’s four wings, which are driven by a set of direct muscles that modulate the left-wing and right-wing pitch asymmetry accordingly. With three or four wing strokes, a tumbling dragonfly can roll 180 degrees and resume flying right-side up. The entire process takes about 200 milliseconds.

“What was difficult was figuring out the key control strategy from the experimental data,” Wang said. “It took us a very long time to understand the mechanism by which a small amount of pitch asymmetry can lead to the observed rotation. The key asymmetry is hidden among many other changes.”

The combination of kinematic analysis, physical modeling and 3D flight simulations now gives researchers a noninvasive way to infer the crucial connections between an animal’s observed behaviors and the internal procedures that control them. These insights can also be used by engineers looking to improve the performance of small flying machines and robots.

“Flight control on the timescale of tens or hundreds of milliseconds is difficult to engineer,” Wang said. “Small flapping machines now can take off and turn, but still have trouble remaining in the air. When they tilt, it is hard to correct. One of the things that animals have to do is precisely solve these kinds of problems.”

The research was supported by the Janelia Research Campus’ Visiting Scientist Program and the Simons Fellowship in Mathematics.

Story Source:

Materials provided by Cornell University. Original written by David Nutt, courtesy of the Cornell Chronicle. Note: Content may be edited for style and length.

Journal Reference:

  1. Z. Jane Wang, James Melfi, Anthony Leonardo. Recovery mechanisms in the dragonfly righting reflexScience, 2022; 376 (6594): 754 DOI: 10.1126/science.abg0946

Cite This Page:

Cornell University. “Dragonflies use vision, subtle wing control to straighten up and fly right.” ScienceDaily. ScienceDaily, 13 May 2022. <www.sciencedaily.com/releases/2022/05/220513113228.htm>.


from New Scientist

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Bats buzz like hornets to scare away predators

Tactic is first known example of a mammal mimicking noise made by an insect

greater mouse-eared bat in flight
The greater mouse-eared bat buzzes like a bee when threatened.HANS CHRISTOPH KAPPEL/MINDEN PICTURES


The whining buzz of a wasp is enough to send many of us running for the hills. Now, it seems that one crafty species has used that aversion to its advantage. Researchers found greater mouse-eared bats mimic the buzzing sound of stinging insects like wasps, likely to scare off predators.

“This is a fascinating study,” says David Pfennig, an evolutionary biologist at the University of North Carolina, Chapel Hill, who studies animal mimicry but who was not involved with the work.

Nature is replete with examples of sneaky animals and plants imitating the traits of other organisms. The innocuous scarlet kingsnake (Lampropeltis elapsoides), for example, has adopted the red-and-black stripes of the dangerously venomous coral snake (Micrurus fulvius).

But there aren’t many noted instances of acoustic mimicry, Pfennig says, likely because they’re hard to study, not necessarily because they don’t exist. “We are a very visually oriented species, and there are a lot of sounds we can’t hear as humans.”

Danilo Russo happened upon one of these by accident. An ecologist at the University of Naples Federico II, he was conducting fieldwork in southeastern Italy more than 2 decades ago when he snagged some greater mouse-eared bats (Myotis myotis). The species is native to Europe and about the size of a house mouse. Every time Russo went to grab the animals and remove them from his nets, “they buzzed like wasps or hornets,” he says. It seemed like some sort of defense mechanism, he explains.

One of the mouse-eared bats’ biggest predators are owls, which commonly live in the tree nooks or rock crevices that wasps, hornets, and other buzzing, stinging insects hole up in. It occurred to Russo that the bats might be buzzing to mimic bees and send owls scurrying away. But it took him several years to find the right bat experts to help answer the question.

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Megafires Are Catastrophically Destructive, But These Microbes Thrive in Them


2 MAY 2022

We know that there are some truly hardy microorganisms out there – able to survive in deep space and deep underground, for example – but a group of microbes identified in a new study might be the most impressively robust yet.

The research describes fungi and bacteria that have not only survived the 2016 Soberanes megafire in California’s redwood tanoak forests but actually thrived as a result of the fire. Understanding how and why this happens could aid recovery efforts for regions affected by wildfires’ devastating impacts.

Further analysis revealed that microbes that did cling on to life and subsequently flourish are genetically linked, a finding that should offer more clues as to why these forms of life are able to make it through the burning.

""Microbes obtained from fire-burned soil. (Jenna Maddox/UCR)

“They have shared adaptive traits that allow them to respond to fire, and this improves our ability to predict which microbes will respond, either positively or negatively, to events like these,” says mycologist Sydney Glassman from the University of California, Riverside.

The soil samples came from plots researchers established in the mid-2000s to study the outbreak of sudden oak death; they first collected samples in 2013, and they compared their contents with samples taken immediately after the fire in 2016.

Not all of the established plots were affected by the fire, so the team even had access to an unburned control plot for comparison.

Overall, there was up to a 70 percent decline in fungi species richness, while bacterial species declined by up to 52 percent per sample. But some bacterial groups, including Actinobacteria (which helps plant material decompose) and Firmicutes (which helps plant growth and controls plant pathogens), ended up thriving.

As for fungi, the heat-resistant Basidioascus yeast saw a massive increase. The yeast degrades various components of wood, including lignin (the tough part of plant cell walls that keeps them structured and protected).

Penicillium is another genus that did rather well out of the fire, and the team of researchers is now keen to figure out how these various microbes grew in number. It’s likely that different types of microbes used different methods.

Penicillium is probably taking advantage of food released from necromass, or ‘dead bodies’, and some species may also be able to eat charcoal,” says Glassman.

Megafires – the term used to describe the historically significant, large-scale fires of recent years that are becoming more intense and covering a wider area – are happening more often as climate change pushes temperatures up and increases snowmelt.

Even though wildfires are a natural part of many ecosystems, they used to be low in severity and pass over an area quickly, helping to revitalize the soil, clear away some dead plants, and help others with their reproduction.

Megafires, however, lead to catastrophic ecosystem damage. The 2016 Soberanes megafire, for example, ended up burning around 132,127 acres or 53,470 hectares of land.

At the moment, not much is known about how soils and their microbiomes respond to megafires, partly because it’s so difficult to predict where the flames will spring up and then travel to.

""The Soberanes megafire in 2016. (CalFire)

The next step for experts is to take the survival strategies offered by these fungi and bacteria and work out how they can be applied to restoration efforts – getting forests back into their previous biodiverse state.

“It’s not likely plants can recover from megafires without beneficial fungi that supply roots with nutrients, or bacteria that transform extra carbon and nitrogen in post-fire soil,” says Glassman. “Understanding the microbes is key to any restoration effort.”

The research has been published in Molecular Ecology.

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Do mushrooms really use language to talk to each other? A fungi expert investigates

Published: April 14, 2022 9.19am EDT


  1. Katie FieldProfessor in Plant-Soil Processes, University of Sheffield

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Katie Field receives funding from NERC, BBSRC, ERC, and the Leverhulme Trust.


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Nearly all of Earth’s organisms communicate with each other in one way or another, from the nods and dances and squeaks and bellows of animals, through to the invisible chemical signals emitted by plant leaves and roots. But what about fungi? Are mushrooms as inanimate as they seem – or is something more exciting going on beneath the surface?

New research by computer scientist Andrew Adamatzky at the Unconventional Computing Laboratory of the University of the West of England, suggests this ancient kingdom has an electrical “language” all of its own – far more complicated than anyone previously thought. According to the study, fungi might even use “words” to form “sentences” to communicate with neighbours.

Almost all communication within and between multi-cellular animals involves highly specialised cells called nerves (or neurones). These transmit messages from one part of an organism to another via a connected network called a nervous system. The “language” of the nervous system comprises distinctive patterns of spikes of electrical potential (otherwise known as impulses), which help creatures detect and respond rapidly to what’s going on in their environment.

Despite lacking a nervous system, fungi seem to transmit information using electrical impulses across thread-like filaments called hyphae. The filaments form a thin web called a mycelium that links fungal colonies within the soil. These networks are remarkably similar to animal nervous systems. By measuring the frequency and intensity of the impulses, it may be possible to unpick and understand the languages used to communicate within and between organisms across the kingdoms of life.

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Using tiny electrodes, Adamatzky recorded the rhythmic electrical impulses transmitted across the mycelium of four different species of fungi.

He found that the impulses varied by amplitude, frequency and duration. By drawing mathematical comparisons between the patterns of these impulses with those more typically associated with human speech, Adamatzky suggests they form the basis of a fungal language comprising up to 50 words organised into sentences. The complexity of the languages used by the different species of fungi appeared to differ, with the split gill fungus (Schizophyllum commune) using the most complicated lexicon of those tested.

A collection of mushrooms with frilly edges.
The split gill fungus is common in rotting wood and is reported to have more than 28,000 sexes. Bernard Spragg/Wikipedia

This raises the possibility that fungi have their own electrical language to share specific information about food and other resources nearby, or potential sources of danger and damage, between themselves or even with more distantly connected partners.

Underground communication networks

This isn’t the first evidence of fungal mycelia transmitting information.

Mycorrhizal fungi – near-invisible thread-like fungi that form intimate partnerships with plant roots – have extensive networks in the soil that connect neighbouring plants. Through these associations, plants usually gain access to nutrients and moisture supplied by the fungi from the tiniest of pores within the soil. This vastly expands the area that plants can draw sustenance from and boosts their tolerance of drought. In return, the plant transfers sugars and fatty acids to the fungi, meaning both benefit from the relationship.

A clump of soil containing fine, white threads.
The mycelium of mycorrhizal fungi enable symbiotic relationships with plants. KYTan/Shutterstock

Experiments using plants connected only by mycorrhizal fungi have shown that when one plant within the network is attacked by insects, the defence responses of neighbouring plants activate too. It seems that warning signals are transmitted via the fungal network.

Other research has shown that plants can transmit more than just information across these fungal threads. In some studies, it appears that plants, including trees, can transfer carbon-based compounds such as sugars to neighbours. These transfers of carbon from one plant to another via fungal mycelia could be particularly helpful in supporting seedlings as they establish. This is especially the case when those seedlings are shaded by other plants and so limited in their abilities to photosynthesise and fix carbon for themselves.

Exactly how these underground signals are transmitted remains a matter of some debate though. It is possible the fungal connections carry chemical signals from one plant to another within the hyphae themselves, in a similar way to how the electrical signals featured in the new research are transmitted. But it is also possible that signals become dissolved in a film of water held in place and moved across the network by surface tension. Alternatively, other microorganisms could be involved. Bacteria in and around fungal hyphae might change the composition of their communities or function in response to changing root or fungal chemistry and induce a response in neighbouring fungi and plants.

The new research showing transmission of language-like electrical impulses directly along fungal hyphae provides new clues about how messages are conveyed by fungal mycelium.

Mushroom for debate?

Although interpreting the electrical spiking in fungal mycelia as a language is appealing, there are alternative ways to look at the new findings.

The rhythm of electrical pulses bears some similarity to how nutrients flow along fungal hyphae, and so may reflect processes within fungal cells that are not directly related to communication. The rhythmic pulses of nutrients and electricity may reveal the patterns of fungal growth as the organism explores its surroundings for nutrients.

Of course, the possibility remains that the electrical signals do not represent communication in any form at all. Rather, charged hyphal tips passing the electrode could have generated the spikes in activity observed in the study.

Small mushrooms with brown, pointy caps growing out of a mossy log.
What on Earth are they talking about? Katie Field, Author provided

More research is clearly needed before we can say with any certainty what the electrical impulses detected in this study mean. What we can take from the research is that electrical spikes are, potentially, a new mechanism for transmitting information across fungal mycelia, with important implications for our understanding of the role and significance of fungi in ecosystems.

These results could represent the first insights into fungal intelligence, even consciousness. That’s a very big “could”, but depending on the definitions involved, the possibility remains, though it would seem to exist on time scales, frequencies and magnitudes not easily perceived by humans.

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Study Examines Insects’ Role in Plastic Pollution


When plastic debris pollutes soil ecosystems, some insects may play a role in spreading it by breaking it down into microplastic particles. A new study sheds light on this dynamic by looking at a variety of soil invertebrates—such as the Zophobas morio beetle larva shown here—and their taste for polystyrene. (Photo by Max Helmberger)

By Paige Embry

Microplastics permeate the world. They can float through the air and have been found in Antarctic ice, the deep ocean, drinking water, and inside an array of animals. Microplastic pollution, mostly in the oceans, has been getting a lot of attention in the last few years but microplastics’ ubiquity means that scientists researching them have to find ways to limit contamination—and assess its extent when it inevitably happens. Max Helmberger, a Ph.D. student in entomology at Michigan State University, has researched several soil-dwelling organisms’ ability to create microplastics from larger plastic debris. He says labs have had to come up with “all sorts of creative solutions” to the contamination problem, with at least one dying all their lab coats bright pink so it would be obvious when bits invade a sample. Helmberger says, “Being persnickity is kind of a must in microplastic research because microplastics are everywhere.”

Microplastics come in two basic forms: primary and secondary. Primary microplastics are ones that are manufactured in sizes smaller than 5 millimeter (think sesame seed). Nurdles, the pre-production pellets used to make plastic products, are an example of a primary microplastic. Secondary microplastics are tiny bits that have broken off larger pieces. It is this second type of microplastic that Helmberger and colleagues recently studied in relation to insects and other invertebrates. Findings from their research were published in February in the open-access Journal of Insect Science.

Helmberger and his colleagues wanted to look at an array of different types of soil-dwelling organisms and assess their ability to fragment plastic in a fairly short period of time. His chosen animals were Acheta domesticus (a house cricket), Oniscus asellus (an isopod, sometimes known as a sowbug or woodlouse), Zophobas morio larvae (a beetle), and Cornu aspersum (a snail). Helmberger put each animal in an “arena”—a small glass jar. The bottom was filled with plaster of Paris and topped with sand that had been heated to 500 degrees Celsius to burn off organics and plastics. The animals went into the jar with pieces of both pristine and weathered polystyrene, along with one oat flake of real food to sustain them. He left them there for 24 hours.

cricket with plastic
isopod with plastic
snail with plastic

Afterward, Helmberger counted the number of microplastic particles in the animal poop, the sand, and within the dead animal itself. To discriminate between the plastics and other tiny bits of stuff in the sample, Helmberger used two fluorescent stains: “Nile red” and a mix of “calcofluor white” and “Evans blue.” Nile red is commonly used to detect microplastics, but Helmberger says, “Nile red also binds to chitin—which, if you study insects, is kind of a problem.” Chitin is a key component in arthropod skeletons, so he needed a way to differentiate between the plastic and chitin. The white/blue mixture was the answer because it binds to chitin but not plastic. Helmberger weeded out anything that fluoresced for both dyes (or only the white/blue mixture). Each particle that fluoresced only under Nile red and also looked like polystyrene was poked with a soldering iron. If it melted or deformed, he knew it was plastic and counted it. Helmberger also set up various anti-contamination protocols, and they largely seemed to work based on the contamination assessment tests he ran, he says.

Helmberger and team found that the beetle larvae were the fragmentation kings, fragmenting both pristine and weathered polystyrene. The crickets and woodlice fragmented only the weathered polystyrene, and the snails “did not appreciably fragment anything.” A second experiment offered the isopod the option of pristine polystyrene, polystyrene exposed to UV rays (as if it had been sitting out in the sun), and polystyrene that had been soaked in a soil suspension. The isopod far preferred the last, showing that the condition of the plastic may play an important role in how tasty a given organism views a piece of plastic.

These experiments produced some expected results—that the beetle larvae fragmented the polystyrene—and some unexpected ones—the snails didn’t. In at least one other experiment, snails did fragment plastic. The researchers speculate that perhaps the difference lay in the snails, which were different species, or in the time the snails were around the plastic, 24 hours in the new study versus four weeks in the past experiment. Helmberger says they picked 24 hours because it seemed like a more realistic amount of time for an organism out in the world to be in contact with a bit of plastic.

This research adds to the evidence that organisms in the environment may not be just passive recipients of microplastic pollution; some may be active creators of it. It also shows how new, and complicated, microplastic research is with protocols still being developed—whether it’s wearing hot pink lab coats or using a soldering iron to figure out what is truly plastic.

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Soil Invertebrates Generate Microplastics From Polystyrene Foam Debris

Journal of Insect Science

Paige Embry is a freelance science writer based in Seattle and author of Our Native Bees: North America’s Endangered Pollinators and the Fight to Save Them. Website: www.paigeembry.com.

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Dead or alive: Microorganisms in soil shape the global carbon cycle

by Lawrence Livermore National Laboratory

<img src="https://scx1.b-cdn.net/csz/news/800a/2022/dead-or-alive-microorg.jpg&quot; alt="Dead or alive: microorganisms in soil shape the global carbon cycle" title="Composition of the soil microbiome and its role in organic matter cycling in different soil habitats. Credit: <i>Nature Reviews Microbiology
Composition of the soil microbiome and its role in organic matter cycling in different soil habitats. Credit: Nature Reviews Microbiology (2022). DOI: 10.1038/s41579-022-00695-z

Whether dead or alive, soil microorganisms play a major role in the biogeochemical cycling of carbon in the terrestrial biosphere. But what is the specific role of death for the bacteria, fungi and microfauna that make up the soil microbiome?

That is the topic of a new review by Lawrence Livermore National Laboratory (LLNL) scientists and collaborators. The article, appearing in Nature Reviews Microbiology, describes how living and dead microorganisms strongly influence terrestrial biogeochemistry by forming and decomposing soil organic matter—the planet’s largest terrestrial stock of organic carbon and nitrogen, and a primary source of other crucial macronutrients and micronutrients.

By shaping the turnover of soil organic matter, soil microorganisms influence atmospheric concentrations of CO2 and the global climate, as well as help provide crucial ecosystem services like soil fertility, carbon sequestration, plant productivity and soil health.

“Our new understanding of how organic matter cycles through soil emphasizes the importance of both living and dead microorganisms in forming soil organic carbon. It is increasingly possible to leverage this understanding within biogeochemical models and to better predict ecosystem functioning under new climate regimes,” said LLNL scientist Noah Sokol, lead author of the paper.

The soil microbiome is the most diverse community in the biosphere, holding at least a quarter of Earth’s total biodiversity. Tens of millions of species of bacteria, archaea, fungi, viruses and microeukaryotes coexist below ground, although only a few hundred thousand have been characterized in detail. A single gram of surface soil can contain more than 109 bacterial and archaeal cells, trillions of viruses and tens of thousands of protists. But the soil microbiome’s influence on biogeochemistry extends well beyond the metabolic activities of living organisms.

“Dead microorganisms accrete in soil as their cellular remains stick to the mineral matrix. Their dead biomass can make up as much as much as 50% of the soil organic matter pool. This means that dead microbial biomass in soil is one of the largest stocks of organic carbon on the planet,” said Jennifer Pett-Ridge, LLNL project lead and head of the Department of Energy’s Office of Science “Microbes Persist” Soil Microbiome Scientific Focus Area (SFA).

New advances in DNA sequencing and isotope tracing are allowing the LLNL team to understand the unique attributes of soil microbes—even those that cannot be cultivated in the laboratory. Though analysis of genetic and biochemical signatures, the team can infer the ecological relationships that control who live, and who die, in complex soil food webs.

Because soil microbial necromass (organic material consisting of, or derived from, dead organisms) represents one of the most globally significant pools of carbon and other nutrients, the authors report that the mechanism and rate of microbial death likely impact terrestrial biogeochemical cycling—an idea they are currently testing in a suite of experiments that are part of LLNL’s Soil Microbiome SFA. The SFA team also is establishing experiments to study how different traits of microorganisms affect organic matter cycling in soils. Team members are working to integrate this trait-based approach into models that predict soil biogeochemical dynamics and enhance the ability to predict changes to the global carbon cycle.

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Team develops microscope to image microbes in soil and plants at micrometer scale

More information: Noah W. Sokol et al, Life and death in the soil microbiome: how ecological processes influence biogeochemistry, Nature Reviews Microbiology (2022). DOI: 10.1038/s41579-022-00695-z

Journal information: Nature Reviews Microbiology 

Provided by Lawrence Livermore National Laboratory 

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Asexual reproduction can have negative effects on genome evolution in stick insects

by Universität zu Köln

<img src="https://scx1.b-cdn.net/csz/news/800a/2022/asexual-reproduction-c.jpg&quot; alt="Asexual reproduction can have negative effects on genome evolution in stick insects" title="Fig. 1. Multiple, independent transitions from sexual to parthenogenetic reproduction are known in the genus <i>Timema</i> , each representing a biological replicate of parthenogenesis, and with a close sexual relative at hand for comparison. (<b>A</b>) Phylogenetic relationships of <i>Timema</i> species. (<b>B</b>) Species sequenced in this study. Photos taken by Bart Zijlstra (<a href="http://www.bartzijlstra.com">www.bartzijlstra.com
Fig. 1. Multiple, independent transitions from sexual to parthenogenetic reproduction are known in the genus Timema , each representing a biological replicate of parthenogenesis, and with a close sexual relative at hand for comparison. (A) Phylogenetic relationships of Timema species. (B) Species sequenced in this study. Photos taken by Bart Zijlstra (www.bartzijlstra.com). Credit: DOI: 10.1126/sciadv.abg3842

An international research team has shown that parthenogenesis, a form of asexual reproduction, negatively affects the genome evolution of the animals that practice it. In this type of reproduction, the offspring are produced from a single unfertilized egg. The study was led by Professor Dr. Tanja Schwander and Professor Dr. Marc Robinson-Rechavi at the University of Lausanne in cooperation with partners at the University of Edinburgh and Dr. Jens Bast at the University of Cologne. The results have been published on 23 February under the title “Convergent consequences of parthenogenesis on stick insect genomes” in Science Advances.

Offspring are produced via two main reproductive pathways: sexual, i.e. fertilization between male and female gametes, or asexual, for example parthogenesis. In parthenogenesis, females pass on their genes without a male being involved. Timema are a genus of stick insects native to western North America, and includes both sexually and asexually reproducing species. The biologists discovered that in asexually reproducing Timema, beneficial mutations cannot be passed on as efficiently in the long term.

Like humans, Timema have a double set of chromosomes. The extent to which these two genome copies differ is described as heterozygosity. During parthenogenesis, however, this difference is lost and the two genome copies become very similar. This reduces variability, which can be important for species to adapt to their environment.

The research team analyzed the genomes of five asexual Timema species and closely related sexually species that reproduce sexually. “The results show that genetic exchange during sexual reproduction promotes the speed of adaptation and genetic diversity in the insects’ natural populations,” said Dr. Jens Bast.

Bast researches the processes of sexual reproduction and the mechanisms of asexuality in the University of Cologne’s “Sex Lab.”

Explore further

Some animal species can survive successfully without sexual reproduction

More information: Kamil S. Jaron et al, Convergent consequences of parthenogenesis on stick insect genomes, Science Advances (2022). DOI: 10.1126/sciadv.abg3842

Journal information: Science Advances 

Provided by Universität zu Köln

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Integrated disease management of black core rot in citrus

What is the problem?
Consumers are caught by surprise when they tuck into a healthy piece of fruit but discover a black rotten mess inside (See fig 1). A new Hort Innovation project aims to shed some light on how this happens in the field so that we can learn how to better manage it.

Black core rot caused by the fungus Alternaria spp. can be a problem for some citrus growers in the southern growing areas in Australia with winter rainfall and cool winter temperatures, contrasting with hot dry summers. Fruit infected with Alternaria spp. can develop black core rot inside the fruit without showing any external symptoms (See Fig 1).

Spores of Alternaria are airborne and they are believed to enter citrus fruit through wounds or micro-cracks at the stylar end during early fruit development after petal fall. After infection of young fruit, the fungus establishes a dormant infection in the stylar end of the fruit.

The problem may not be detected until after harvest when the fruit reaches the consumer or the juicing plant. Besides the internal black rot, the fruit also develops a bitter flavour. In addition to turning the inside of the fruit black the disease can also give rise to early fruit drop resulting in yield loss (see Fig 2).

 Figure 1: Black core rot in mandarin.

What is the problem and impact from a grower’s perspective?
Application of fungicides is at present not giving consistent control and one way for growers to reduce the impact of the disease is to delay harvesting until most of the infected fruit have dropped.

Project leader Professor Andre Drenth explains: “Growers have to make a decision to apply fungicides before knowing that they will have the problem. If the decision is made to take a pro-active approach based on black core rot problems experienced in previous years in certain blocks, there is no solid base on which decisions concerning choice of product, timing and frequency of application can be made.”

“The return on investment will only become evident after harvest and even then, the effectiveness of applied management strategies is hard to determine.”

What would help growers better control this disease?
The risk of losses due to black core rot would be reduced by knowing which environmental conditions and crop stage have the highest risk of infection for certain varieties and information on which products to apply and the timing of application.

What is this project investigating?
This project will start with a survey and interviews with growers and industry stakeholders to get a better handle on the occurrence and impact of black core rot in citrus and capture the effectiveness and limitations of current practices that are used and favoured among citrus growers for managing citrus black core rot.

Figure 2: Fallen fruit with Black core rot.

For more information: citrusaustralia.com.au

Publication date: Tue 22 Feb 2022

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‘Simple’ bacteria found to organize in elaborate patterns

Date:January 6, 2022Source:University of California – San Diego Summary: Researchers have discovered that biofilms, bacterial communities found throughout the living world, are far more advanced than previously believed. Scientists found that biofilm cells are organized in elaborate patterns, a feature that previously only had been associated with higher-level organisms such as plants and animals.Share:FULL STORY

Bacteria illustration (stock image).Credit: © SciePro / stock.adobe.com

Over the past several years, research from University of California San Diego biologist Gürol Süel’s laboratory has uncovered a series of remarkable features exhibited by clusters of bacteria that live together in communities known as biofilms.

Biofilms are prevalent in the living world, inhabiting sewer pipes, kitchen counters and even the surface of our teeth. A previous research study demonstrated that these biofilms employ sophisticated systems to communicate with one another, while another proved biofilms have a robust capacity for memory.

Süel’s laboratory, along with researchers at Stanford University and the Universitat Pompeu Fabra in Spain, has now found a feature of biofilms that reveal these communities as far more advanced than previously believed. Biological Sciences graduate student Kwang-Tao Chou, former Biological Sciences graduate student Daisy Lee, Süel and their colleagues discovered that biofilm cells are organized in elaborate patterns, a feature that previously only had been associated with higher-level organisms such as plants and animals. The findings, which describe the culmination of eight years of research, are published Jan. 6 in the journal Cell.

“We are seeing that biofilms are much more sophisticated than we thought,” said Süel, a UC San Diego professor in the Division of Biological Sciences’ Section of Molecular Biology, with affiliations in the San Diego Center for Systems Biology, BioCircuits Institute and Center for Microbiome Innovation. “From a biological perspective our results suggest that the concept of cell patterning during development is far more ancient than previously thought. Apparently, the ability of cells to segment themselves in space and time did not just emerge with plants and vertebrates, but may go back over a billion years.”

Biofilm communities are made up of cells of different types. Scientists previously had not thought that these disparate cells could be organized into regulated complex patterns. For the new study, the scientists developed experiments and a mathematical model that revealed the genetic basis for a “clock and wavefront” mechanism, previously only seen in highly evolved organisms ranging from plants to fruit flies to humans. As the biofilm expands and consumes nutrients, a “wave” of nutrient depletion moves across cells within the bacterial community and freezes a molecular clock inside each cell at a specific time and position, creating an intricate composite pattern of repeating segments of distinct cell types.

The breakthrough for the researchers was the ability to identify the genetic circuit underlying the biofilm’s ability to generate the biofilm community-wide concentric rings of gene expression patterns. The researchers were then able to model predictions showing that biofilms could inherently generate many segments.

“Our discovery demonstrates that bacterial biofilms employ a developmental patterning mechanism hitherto believed to be exclusive to vertebrates and plant systems,” the authors note in the Cell paper.

The study’s findings offer implications for a multitude of research areas. Because biofilms are pervasive in our lives, they are of interest in applications ranging from medicine to the food industry and even the military. Biofilms as systems with the capability to test how simple cell systems can organize themselves into complex patterns could be useful in developmental biology to investigate specific aspects of the clock and waveform mechanism that functions in vertebrates, as one example.

“We can see that bacterial communities are not just globs of cells,” said Süel, who envisions research collaborations offering bacteria as new paradigms for studying developmental patterns. “Having a bacterial system allows us to provide some answers that are difficult to obtain in vertebrate and plant systems because bacteria offer more experimentally accessible systems that could provide new insights for the field of development.”

Coauthors of the paper include: Kwang-Tao Chou (UC San Diego graduate student), Dong-yeon Lee (former UC San Diego graduate student, now a postdoctoral scholar at Stanford University), Jian-geng Chiou (UC San Diego postdoctoral scholar), Leticia Galera-Laporta (UC San Diego postdoctoral scholar), San Ly (former UC San Diego researcher), Jordi Garcia-Ojalvo (Universitat Pompeu Fabra Professor) and Gürol Süel (UC San Diego Professor).

Story Source:

Materials provided by University of California – San Diego. Original written by Mario Aguilera. Note: Content may be edited for style and length.

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Journal Reference:

  1. Kwang-Tao Chou, Dong-yeon D. Lee, Jian-geng Chiou, Leticia Galera-Laporta, San Ly, Jordi Garcia-Ojalvo, Gürol M. Süel. A segmentation clock patterns cellular differentiation in a bacterial biofilmCell, 2022; 185 (1): 145 DOI: 10.1016/j.cell.2021.12.001

Cite This Page:

University of California – San Diego. “‘Simple’ bacteria found to organize in elaborate patterns.” ScienceDaily. ScienceDaily, 6 January 2022. <www.sciencedaily.com/releases/2022/01/220106111601.htm>.

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