ReportWire

Tag: Microbiome

  • Starting small to better understand key steps in the carbon cycle

    Starting small to better understand key steps in the carbon cycle

    [ad_1]

    Newswise — December 14, 2022 – Earth’s carbon cycle works on a global scale. But it can be affected by the tiniest of organisms: soil microbes. These microbes decompose organic matter like plant litter and dead organisms, and create simple carbon compounds. These simple carbon compounds can then be used by other organisms, or turned into gases (like carbon dioxide) and released into the atmosphere.

    Much like us, soil microbes can be picky about where they live and work. “Just as we may prefer a certain range of temperature and humidity, soil microbes have their preferable conditions too,” says Alyssa Kim, a researcher at Cornell University.

    Kim is the lead author of a new study that explores how soil conditions, like moisture level and pore size, can affect soil microbes. Understanding how different soil conditions impact microbial activity can give researchers a better handle on ways to increase soil health and fertility, and help combat climate change. For example, “it can be a critical part in reducing greenhouse gas emissions from agricultural fields after harvests,” says Kim.

    Kim recently presented her work at the 2022 ASA-CSSA-SSSA annual meeting, held in Baltimore, Maryland.

    Kim and her colleagues at Michigan State University compared microbial activity near corn and switchgrass leaf litter. Corn is a vital crop, and farmers in the United States planted nearly 90 million acres in the 2022 growing year. Switchgrass is a promising bioenergy crop with an expanding footprint. “Also, corn and switchgrass have different litter characteristics,” says Kim. “Litter chemistry affects how easily microbes can decompose different litters. The physical characteristics like texture can affect the water and air environment near litters.”

    Kim and her colleagues found that corn and switchgrass litters differ in how they change moisture levels in the soil near them. “We found distinct moisture depletion 0.1 to 1.5 millimeter away from switchgrass residues,” says Kim.

    To study this moisture distribution, Kim used a method called X-ray and Neutron computed tomography. This method works very similarly to medical CT scans. “It’s a very promising, non-destructive way to study soils and water in them,” says Kim.

    It turns out, moisture content is one of the most important factors influencing soil microbial activity. That’s because one way that microbes decompose organic material, like leaf litter, is by releasing chemicals called enzymes. Different enzymes break down different materials. For example, an enzyme called beta-glucosidase can break down plant cell walls. Another enzyme called chitinase can break down the exoskeletons of insects and some fungi. Once the enzymes break down their target materials into simpler chemicals, soil microbes can feast.

    “When soil moisture levels are optimal for microbes, they tend to produce more enzymes,” says Kim. That can lead to faster decomposition of leaf litter and the release of larger amounts of carbon dioxide. That’s exactly what Kim and her colleagues observed. Soil moisture levels were higher near corn litter, and decomposing corn litter released more carbon dioxide quicker than switchgrass litter.

    Although the study focused on millimeter-scale observations, it has large-scale implications. “Studying these microscale dynamics can help us to understand what is actually happening in our vast corn fields, and also, in promising bioenergy cropping systems like switchgrass,” says Kim.

    Kim also tested how soil pore size affects microbial enzyme activity. These pore sizes ranged from 10 to 30 micrometers, slightly smaller than the thickness of a single strand of most human hair. “It is crucial to study soil pore structures because that’s where soil microbes live,” says Kim.  Kim used a method called Zymography, to map the activity of different enzymes. “We add some chemicals onto the soil surface. Such chemicals show fluorescence when decomposed, and that is how we detect the location of enzymes.”

    Soil pore size affects different enzymes differently. Beta-glucosidase – the enzyme that breaks down plant cell walls – worked more efficiently in soils with smaller pores. On the other hand, chitinase enzyme activity was higher in soils with larger pore sizes. “These contrasting results tell us that what is decomposed in soils can depend on soil pore architecture,” says Kim. “That’s because there are different microbes living in pores of different sizes, producing different enzymes.”

    Soils in farm fields have a mix of large and small pores, which indicates a mix of moisture levels and different microbes. “In the future, I would like to look at soil pores and moisture levels on larger scales and test how differences in moisture distribution affects the decomposition process,” says Kim.

    This research was supported by Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (Award DE – SC0018409); National Science Foundation Long-term Ecological Research Program (DEB 1832042) at the Kellogg Biological Station; Michigan State University AgBioResearch; and special thanks to Dr. Sasha Kravchenko and Kravchenko Lab at Michigan State University, as well as Anders Kaestner at Paul Scherrer Institute in Switzerland.

    [ad_2]

    American Society of Agronomy (ASA), Crop Science Society of America (CSSA), Soil Science Society of America (SSSA)

    Source link

  • Microphytobenthos in the Dutch Wadden Sea feeds on ‘left-overs’ in the bottom

    Microphytobenthos in the Dutch Wadden Sea feeds on ‘left-overs’ in the bottom

    [ad_1]

    Isotopes
    Newswise — For the study, Riekenberg and colleagues looked at the chemical variations in the isotopes of nitrogen. There are two predominate forms of nitrogen, ‘nitrogen-14’ and the heavier version, ‘nitrogen-15’. When an organism digests protein, for example from plankton, the resulting nitrogen is used to create its own proteins. In this process, the lighter nitrogen-14 is lost a bit, so the relative concentration of the heavy nitrogen increases a little at each step in the food chain. As a result, animals higher up the food chain retain relatively more and more nitrogen-15.

    Individual amino acids
    In recent years, it has become possible to also analyze the different nitrogen isotopes from individual amino acids. Certain amino acids (the building blocks of protein) cannot be created by higher organisms themselves. As a result, those essential or ‘source amino acids’ need to be obtained from the diet and remain mostly unchanged throughout the food chain. Therefore, in these amino acids, the stable isotope ratio of nitrogen does not become progressively higher with each step of eating or being eaten. Other, so-called trophic amino acids do change a lot during metabolism through each step of the food chain. Thus, the difference in nitrogen composition between trophic and essential amino acids provides a measure of how high up the food chain an organism is, independent of any variations in underlying nitrogen sources supporting the ecosystem. We used this technique to build a trophic structure from direct measurements of the Dutch Wadden Sea food web.   

    Detritus in the pore water
    Using samples that were collected between 2011 and 2014 during the long-lasting monitoring program of NIOZ, SIBES (the Synoptic Intertidal BEnthic Survey), Riekenberg analyzed the nitrogen isotopes of amino acids from 340 different animals from across the Dutch Wadden Sea. Thus, he was able to trace back the sources of nitrogen that these animals used. Riekenberg: “We saw that quite a bit of the nitrogen did not come from the overlying water column, but from the benthic primary producers, like diatoms, using nitrogen from the pore water at the bottom of the Wadden Sea. This nitrogen has a distinct signal, since it is what remains after the breaking down of organic matter and denitrification, and can therefore be tracked into a portion of the food web.”

    Ecological models
    Riekenberg stresses that this new piece of the jigsaw adds important knowledge to the science of the Wadden Sea ecosystem. “Now that we know that detrital nitrogen in porewaters is an important direct source of nutrients, this should be included in ecological models we make of the Wadden Sea. If our models do not include all pools of nutrients supporting the food web, then how can these models accurately reflect the ecology of the Wadden Sea when they are used to predict future impacts or changes?”

    [ad_2]

    Royal Netherlands Institute for Sea Research

    Source link

  • Having good friendships may make for a healthier gut microbiome

    Having good friendships may make for a healthier gut microbiome

    [ad_1]

    Newswise — Social connections are essential for good health and wellbeing in social animals, such as ourselves and other primates. There is also increasing evidence that the gut microbiome – through the so-called ‘gut-brain axis’ – plays a key role in our physical and mental health and that bacteria can be transmitted socially, for example through touch. So how does social connectedness translate into the composition and diversity of the gut microbiome? That’s the topic of a new study in Frontiers in Microbiology on rhesus macaques, Macaca mulatta.

    Lead author Dr Katerina Johnson, a research associate at the Department of Experimental Psychology and the Department of Psychiatry of the University of Oxford, said: “Here we show that more sociable monkeys have a higher abundance of beneficial gut bacteria, and a lower abundance of potentially disease-causing bacteria.”

    Monkey island

    The scientists focused on a single social group (with 22 males and 16 females between the ages of six and 20 years) of rhesus macaques on the island of Cayo Santiago, off the eastern coast of Puerto Rico. Macaques originally only lived in North Africa and Asia. But in 1938, a founder population of 409 rhesus macaques was moved from India to Cayo Santiago. Today, more than 1,000 macaques live on the 15.2 hectare island, divided into several social groups. They range and forage freely, although their diet gets supplemented daily with monkey chow. Researchers do behavioral observations on the monkeys each year.

    Between 2012 and 2013, the authors collected a total of 50 uncontaminated stool samples from this social group. As a measure of social connectedness, they used the time each monkey spent grooming or being groomed in 2012 and 2013, and his or her number of grooming partners.

    Social grooming

    Co-author Dr Karli Watson, from the Institute of Cognitive Science at the University of Colorado Boulder, explained: “Macaques are highly social animals and grooming is their main way of making and maintaining relationships, so grooming provides a good indicator of social interactions.”

    Johnson, Watson et al. analyzed DNA sequence data from the stool samples to measure the composition and diversity of the gut microbial community, and looked at the relationship with social connectivity. They also took into account sex, age, season, and rank within the group’s hierarchy. They focused on microbes that have been repeatedly shown in to be either more or less abundant in people or rodents with autism-like symptoms (commonly accompanied by social disconnection) or which are socially deprived.

    Sociable monkeys have more ‘good’ microbes

    “Engagement in social interactions was positively related to the abundance of certain gut microbes with beneficial immunological functions, and negatively related to the abundance of potentially pathogenic members of the microbiota,” said co-author Dr Philip Burnet, a professor from the Department of Psychiatry at the University of Oxford.

    For example, genera more abundant in the most sociable monkeys included Faecalibacterium and Prevotella. Conversely, the genus Streptococcus, which in humans can cause diseases such as strep throat and, pneumonia, was most abundant in less sociable monkeys.

    “It is particularly striking that we find a strong positive relationship between the abundance of the gut microbe Faecalibacterium and how sociable the animals are. Faecalibacterium is well known for its potent anti-inflammatory properties and is associated with good health,” said Johnson.

    Cause and effect?

    But what drives the relationship between social connectedness and gut microbiome composition? Distinguishing between cause and effect isn’t easy.

    “The relationship between social behavior and microbial abundances may be the direct result of social transmission of microbes, for example through grooming. It could also be an indirect effect, as monkeys with fewer friends may be more stressed, which then affects the abundance of these microbes. As well as behavior influencing the microbiome, we also know it is a reciprocal relationship, whereby the microbiome can in turn affect the brain and behavior,” said Johnson.

    Co-author Dr Robin Dunbar, a professor from the Department of Experimental Psychology at the University of Oxford, said: “As our society is increasingly substituting online interactions for real-life ones, these important research findings underline the fact that as primates, we evolved not only in a social world but a microbial one as well.”

    [ad_2]

    Frontiers

    Source link

  • Researchers transform popcorn into microbiome-boosting superfood

    Researchers transform popcorn into microbiome-boosting superfood

    [ad_1]

    Newswise — A Nebraska-led coming attraction may soon pop into a global blockbuster.

    Through a decade-long project supported by Conagra Foods, a University of Nebraska–Lincoln research team led by David Holding has naturally bred new varieties of popcorn that outperform today’s most popular kernels in their intrinsic nutritional value and taste.

    “When we took on this challenge, I was 50% confident that we could deliver on improvements in terms of nutrition,” Holding said. “But at no time did I think this would lead us to a level of success that also delivered improved taste, texture and prebiotics over conventional popcorn.”

    The Nebraska-made varieties — which are currently being tested by Conagra — offer nearly twice the level of lysine, an amino acid essential in the diets of humans and livestock, compared to popular popcorn varieties and other cereal grains.

    Higher lysine can enhance nutritional value, thus adding economic value and broadening the appeal of the popular snack, Holding said.

    Dent corn, a worldwide crop and the signature variety of the Midwest, is deficient in lysine. But in the 1990s, researchers successfully bred a gene variant known as opaque-2 into dent corn. In lowering the production of normally dominant prolamin proteins, opaque-2 allowed for a rise in non-prolamins: those containing lysine and another essential amino acid, tryptophan. The resulting variety — Quality-Protein Maize, or QPM — has since helped combat malnutrition in many developing countries.

    With the backing of Conagra Foods, Holding decided to try the same in popcorn.

    “It turns out that that’s really difficult to do,” said Holding, professor and associate department head in the Department of Agronomy and Horticulture.

    The problem was at once simple and complex: Popcorn containing opaque-2 wouldn’t pop. And that problem stemmed from what’s in its name: Opaque-2 tends to turn popcorn’s normally hard, glassy kernels into softer, chalkier forms resistant to popping.

    Agronomists had previously managed to breed the undesirable softness trait out of the QPM dent corn, which was otherwise more susceptible to pests and harvesting damage. But they did so mostly without knowing which genes helped restore the kernels’ glassy consistency.

    Holding had devoted considerable time to identifying swaths of the corn genome responsible for restoring that glassiness. So he set out to cross-breed multiple generations of the QPM dent corn with popcorn varieties selected to contain the restorative genes.

    The outcome? High-lysine Quality Protein Popcorn (QPP) that pops as well as the original variety.

    “When this project started, I wasn’t sure we could achieve that, given that people hadn’t been very successful in transferring beneficial traits from dent corn to popcorn in the past,” Holding said. “We’re the first to take the dent QPM variety and successfully convert that into popcorn, achieving high lysine and maintaining popping.

    “This is a product that lends itself to organic production and can be marketed as a novel popcorn variety, as consumers are paying more attention to their foods’ nutritional value. For popcorn breeding in general, this also shows the potential for mining other traits from dent corn into popcorn to improve the crop’s agronomic performance.”

    Other advancements include blind taste testing — many of the Nebraska QPP hybrids outperformed the non-QPP lines in terms of taste and texture — and working with the Nebraska Food for Health Center to show positive prebiotic impacts of the popcorn.

    “What we’ve developed here is a complete protein snack that can be marketed as a superfood due to its positive prebiotic qualities,” Holding said. “And it isn’t just a snack food. It is also quite nutritious and could be beneficial as a dietary supplement in developing countries where protein is needed.

    “This work has truly been much more successful than we expected.”

    [ad_2]

    University of Nebraska-Lincoln

    Source link

  • Controlling Gut Flora Can Reduce Mortality in Critically Ill Patients on Life Support

    Controlling Gut Flora Can Reduce Mortality in Critically Ill Patients on Life Support

    [ad_1]

    Newswise — Preventing severe lung infections in mechanically ventilated intensive care patients by applying topical antibiotics to the upper digestive tract results in a clinically meaningful improvement in survival, new research shows. 

    The results are being presented during the ‘Hot Topics’ session of the European Society of Intensive Care Medicine annual congress in Paris and simultaneously published in the Journal of the American Medical Association (JAMA).

    Professor John Myburgh AO, lead author and Director of the Critical Care Division at The George Institute for Global Health, said that ventilator-associated pneumonia is a major cause of death and disability in critically ill patients being mechanically ventilated in intensive care units.

    “While the concept of ‘selective decontamination’ of the digestive tract, or ‘SDD’, has been around for decades, this is the first large-scale randomised clinical trial that used a high-quality commercially prepared product specifically designed to prevent ventilator-associated pneumonia in these patients,” he said.

    “In nearly 3,000 patients treated with SDD, we saw a reduction in death of around two percent, equivalent to one death prevented for every 50 patients treated.”

    SDD is an infection-control measure where non-absorbed antibiotics and antifungal agents are applied to the mouth and stomach, combined with a short course of intravenous antibiotics.

    This inhibits the development of ventilator-associated pneumonia caused by harmful bacteria and overgrowth of fungi that normally live in the upper part of the gut but enter and infect the lungs once patients are placed on a ventilator.

    While SDD may reduce infections and prevent deaths, it has not been widely adopted as the evidence was not considered strong enough and there are widely held concerns about the potential risk of causing antibiotic resistance.

    To address this uncertainty, the Selective Decontamination of the Digestive tract in the Intensive Care Unit (SuDDICU) trial was designed to determine whether adding SDD to the usual care of ICU patients would reduce all-cause hospital mortality compared to usual care alone.

    The SuDDICU trial recruited 5,982 mechanically ventilated adults from 19 ICUs in Australia between April 2018 and May 2021. Each ICU delivered either SDD with usual care or usual care alone for 12 months and then crossed over to the other option for a second 12-month period.

    The study found that while SDD with standard care compared to standard care alone did not result in a statistically significant reduction in in-hospital mortality (27.0% vs 29.1% respectively), the range of values included a clinically important benefit.

    “Moreover, we saw that SDD was also associated with a significant reduction in new hospital-acquired infections and there were no adverse events related to the administration of SDD itself,” said Professor Myburgh.

    George Institute investigators combined the results with those of other major randomised clinical trials of SDD conducted over the last 20 years in a systematic review and meta-analysis, also being published in JAMA and presented at the conference by senior author, Associate Professor Anthony Delaney.

    “This review provides a high degree of certainty for clinicians to administer SDD to critically ill, mechanically ventilated patients in their ICUs to reduce the incidence of ventilator-associated pneumonia and the potential increased risk of death,” A/Prof Delaney said.

    Professor Myburgh added that SDD alongside other important strategies reinforces the importance of effective and safe preventive medicine in this vulnerable patient population.

    “We now plan to extend our trial to low and middle-income countries where mortality rates and the incidence of infections with antimicrobial resistant organisms are higher,” he said.

    [ad_2]

    George Institute for Global Health

    Source link