Nitrogen is an essential building block of proteins, amino acids, and DNA. Without nitrogen, cells can’t function or reproduce. Nitrogen is abundant in the atmosphere as dinitrogen gas, but plants and animals can’t access atmospheric nitrogen. Instead, we rely on biologically available forms like ammonia and nitrate.
Specialized microbes can transform atmospheric nitrogen into ammonia via a process called biological nitrogen fixation. Nitrogen-fixing soil bacteria have a unique protein complex, the nitrogenase complex, that facilitates this nitrogen transformation. The nitrogenase complex is activated by a group of genes known as nif genes.
Legume plants like peanuts, peas, and beans have nitrogen-fixing bacteria in the soil zone around their roots, called the rhizosphere. The symbiotic relationship between nitrogen-fixing soil bacteria and legume plants supplies most of the biologically available nitrogen to life on Earth.
Bacteria attached to plant roots “feed” nitrogen to plants through the soil, and in turn receive organic acids for energy from plants performing photosynthesis. Source: Wikimedia Commons
However, one piece of the puzzle remains unexplored: the role of soil viruses in these nitrogen transformations, referred to as the nitrogen cycle. Viruses are microscopic particles made up of genetic material and proteins, but they can’t reproduce without a host cell. Scientists consider viruses to be biological entities that are halfway between living and non-living.
To reproduce, viruses contact a host cell and inject their genetic material into it. The virus’s genetic material takes over the host cell’s genome and forces the cell to produce proteins that assemble into new viruses. As new viruses are created, they can incorporate genes from the host cell into their own genetic material. Genes that are transferred from a host cell to a virus are known as auxiliary metabolic genes (AMGs). Viruses can carry AMGs and pass them to other hosts or use them to increase their own ecological fitness.
Scientists from China, Spain, and the Czech Republic set out to investigate whether viruses from legume roots could increase local soil nitrogen fixation by expressing nif AMGs or by transferring nif genes to other bacteria. First, they determined the global distribution of viral nitrogen-fixing genes by analyzing about 8.6 million viral genomes from the Integrated Microbial Genomes/Virus database. They looked for the DNA sequences of known nitrogen-fixing genes and the locations where the viruses were sampled. They found that only 0.003% of the viruses in the database had at least 1 nitrogen-fixing gene, but they clustered in the same locations as nitrogen-fixing bacteria.
The team also found 3 types of viruses that most commonly carried nitrogen-fixing genes: Kyanoviridae, Nudiviridae, and Bronfenbrennervirinae. Kyanoviridae viruses carried a nif gene called nifU. The researchers used a computer program called DRAM-v to confirm that nifU was a fully functional gene and a real tool that viruses could use.
Next, the team collected soil samples from a cowpea field in Nanjing, China, to test whether the cowpea roots influenced the abundance of viruses using nitrogen-fixing genes. They collected soil from the cowpea rhizospheres and soil away from the plants. They analyzed both viral and bacterial RNA in the soil samples to identify active genes, using a sequencing process called metatranscriptomics. They found that the viral nifU gene was actively expressed in the cowpea rhizosphere samples more than in the non-crop soil. Although about 96% of nifU genes were being expressed by bacteria, viruses contributed about 4%.
The researchers then assessed whether rhizospheric viruses changed the amount of nitrogen being fixed in these soils. They set up small, enclosed containers of sterile soil and added either bacteria or a mixture of bacteria and viruses extracted from the cowpea rhizospheres. They found that soil with viruses had higher total nitrogen (36 milligrams per kilogram, or mg/kg) than soil without viruses (17 mg/kg).
Finally, they adjusted the air in each container to have a different form of dinitrogen gas. Atoms of the same element that have different atomic masses are known as isotopes. Nitrogen has 2 stable isotopes: lighter nitrogen-14 and heavier nitrogen-15. Bacteria or viruses that fix nitrogen at natural isotope abundances will take up nitrogen-14. But scientists can track who in the population fixes nitrogen by adding nitrogen-15 to the air, a process called nitrogen-15 stable isotope probing. Nitrogen-fixers will incorporate the heavy nitrogen-15 into their biomass over time and increase their weight, allowing researchers to separate and identify them.
The team grew the bacteria and viruses with nitrogen-15 for 35 days, then used stable isotope probing to separate the nitrogen fixers. They detected viral nifU AMGs among the heavier biomass, confirming that rhizospheric viruses were fixing nitrogen.
The team concluded that rhizospheric viruses and the viral nifU AMG can increase nitrogen fixation in cowpea soils. The team suggested that although viruses with nitrogen-fixing genes are rare, they can influence the soil nitrogen cycle. They recommended that future researchers further test the contribution of viral nifU genes to plant nitrogen fixation with controlled infection experiments.
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They could complicate the hunt for extraterrestrial life—and compromise astronaut health
The post All the Microbes That Could Survive in Space appeared first on Nautilus.
Scientists have uncovered a shared target used by multiple diarrhea-causing bacteria to invade the gut. Despite decades of research, scientists still do not have vaccines against two of the world’s most common causes of severe bacterial diarrhea: enterotoxigenic E. coli (ETEC) and Shigella. Together, these pathogens infect hundreds of millions of people each year and [...]A new study suggests that altering the gut microbiome with probiotics may provide additional benefits for older adults being treated for depression. Could a daily probiotic help ease depression in older adults? A new clinical trial suggests the answer may be yes, adding to growing evidence that the gut and brain are more connected than [...]In a groundbreaking advance at the intersection of bioengineering and microbiology, researchers at Harvard’s John A. Paulson School of Engineering and Applied Sciences have unveiled a pioneering device known as a pico-calorimeter. This remarkable instrument is capable of directly detecting heat signals emanating from minute populations of living cells, a feat that until now has remained technologically elusive due to the vanishingly small scale of these thermal signatures. By enabling real-time metabolic tracking at unprecedented sensitivity, the pico-calorimeter promises to revolutionize our understanding and monitoring of cellular activity, bacterial growth, and antibiotic response.
At the core of this innovation is the principle that living cells, as they metabolize nutrients, grow, divide, and react to external stimuli such as drugs, intrinsically emit heat. This metabolic heat, although incredibly subtle, offers a direct, unmediated insight into the physiological state of cells. Unlike conventional methods that infer cellular metabolism indirectly through oxygen consumption or chemical byproducts, the pico-calorimeter provides a direct calorimetric measurement, offering a more immediate and accurate assay of cellular energetics.
The technical architecture of the device is a marvel of microengineering. It consists of three ultrafine glass capillaries aligned on a delicately micromachined membrane with near-atomic precision. One of these capillaries harbors the biological sample suspended in a liquid growth medium, while the remaining two serve as thermodynamic reference points. As the bacteria or other cells within the sample metabolize and proliferate, they release minute quantities of heat. This thermal flux generates infinitesimal temperature gradients relative to the reference capillaries, which are then transduced into electrical signals by a nearby thermopile—an exquisitely sensitive heat-to-electricity converter capable of resolving fluctuations on the order of picowatts.
A critical enhancement in this iteration of the pico-calorimeter lies in its housing within a vacuum chamber. This vacuum environment thermally isolates the sensor assembly from ambient thermal noise, dramatically amplifying sensitivity by nearly an order of magnitude compared to antecedent designs. The prior versions employed liquid droplets on suspended membranes, which, while innovative, presented operational challenges and limited sensitivity. The current vacuum-sealed, microfluidic integration advances robustness, usability, and measurement fidelity, marking a milestone in the delicate art of thermal detection at the cellular scale.
Demonstrating the device’s prowess, the research team employed the pico-calorimeter to monitor Escherichia coli growth dynamics, beginning with an initial seed population as modest as thirty to forty individual bacterial cells. This capability to detect and analyze such small biological communities unveils immense potential for applications ranging from fundamental microbiology to clinical diagnostics. Notably, the device was employed to examine bacterial metabolic responses upon introduction of antibiotics with varying mechanisms of action—chloramphenicol, rifampicin, and ampicillin—capturing differential heat signatures indicative of altered cellular viability and activity.
These direct calorimetric measurements have revealed metabolic perturbations well in advance of what traditional culture-based microbiological assays could discern. This capability is particularly transformative in clinical scenarios such as sepsis, where detecting and characterizing bacterial populations at extremely low concentrations in blood is vital but presently time-consuming. The pico-calorimeter’s sensitivity could drastically truncate diagnostic timelines from days to hours, allowing more timely and targeted antimicrobial interventions.
Beyond measuring growth and antibiotic susceptibility, the pico-calorimeter enables continuous, real-time monitoring of fundamental cellular parameters including viability, proliferation rate, and stress responses. This temporal resolution offers researchers the invaluable ability to dynamically track cellular states and transitions, capturing metabolic shifts as cells respond to environmental perturbations or pharmacological treatments. Such insights may open new frontiers in cell biology, pharmacodynamics, and personalized medicine.
This breakthrough device represents the culmination of roughly two decades of meticulous research in the Vlassak laboratory, with contributions building from initial exploration of nano-calorimetry techniques aimed at materials science phenomena such as phase transitions in shape memory alloys and metallic glasses. The interdisciplinary bridge extended to biological systems has ushered in ultrasensitive calorimetry methods capable of assessing metabolic heat production in large cells and complex embryonic development processes, laying foundational expertise for this current bio-calorimetric leap.
Technologically, the fabrication of the pico-calorimeter draws upon state-of-the-art micro- and nanofabrication facilities, including the Harvard Center for Nanoscale Systems. The integration of microfluidics and micromachined sensing elements within thermally isolated environments exemplifies the cutting-edge convergence of materials science, electrical engineering, and biological instrumentation. The multidisciplinary synergy underscores the technological sophistication essential for detecting thermal signals billions of times smaller than everyday heat fluxes.
Commercially, the Harvard Technology Development office has filed multiple patents covering the pico-calorimeter and its applications in antimicrobial susceptibility testing. Juanjuan Zheng, a pivotal figure in this research and founder of an innovative startup, is leveraging the technology to deliver practical, label-free, real-time metabolic readouts. These tools hold promise for broad adoption in life sciences research, pharmaceutical development, and clinical diagnostics, harnessing the power of heat measurement to glean functional insights from minute biological samples.
As the research community embraces this transformative platform, interest has surged from a diverse array of scientific domains. The ability to capture direct metabolic information from tiny, dynamic living systems resolves a long-standing challenge in single-cell and small-population analysis. This heralds a new era where functional metabolic data provides early and actionable information on biological states, ranging from cellular growth and stress response to drug efficacy and resistance patterns.
In essence, the Harvard pico-calorimeter transcends conventional bioanalytical tools by transforming infinitesimal heat emissions into a vivid metabolic narrative. This technological breakthrough not only augments our scientific toolkit but also possesses the potential to accelerate biomedical discovery, enhance therapeutic precision, and ultimately improve patient outcomes by enabling rapid, noninvasive interrogation of cellular function. The implications for healthcare, research, and biotechnology are profound, heralding an exciting frontier where the subtle warmth of life becomes an unequivocal signal of cellular health and response.
Subject of Research: Cells
Article Title: A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing
References: Proceedings of the National Academy of Sciences
Image Credits: Vlassak Group / Harvard SEAS
Keywords: Calorimetry, Chemical analysis, Life sciences, Biophysics, Single cell profiling, Single molecule analysis, Materials science, Physics, Applied sciences and engineering, Applied physics, Engineering, Electrical engineering, Chemical engineering, Mechanical engineering, Health and medicine, Biomedical engineering
As our world is rapidly reshaped by climate change, glaciers have retreated and revealed new swaths of bare land. Throughout the coming decades to centuries, this rocky ground will become dappled with lichens and scrub, eventually giving rise to newborn forests in a process known as ecological succession.
Ecologists have mapped out the stages of ecological succession for plant communities, observing which species are the first to colonize land and how these pioneer species promote secondary growth. Yet before any plants sink their roots into the soil, it is populated by thriving communities of single-celled microbes that prepare it for further habitation. Scientists study how these microbial communities arise to understand how healthy ecosystems develop.
Newly exposed land is nutrient-poor and subject to large temperature fluctuations, so the first species to settle there must overcome these challenges. Pioneer plant species are often habitat generalists, meaning they can thrive under a variety of environmental conditions. However, all plants convert water and sunlight into carbon and energy. Microbes can use many different energy sources, and often contain genes for multiple metabolisms in their genomes. Therefore, researchers wondered whether pioneer microbes could also be defined by their metabolic flexibility.
A team of scientists based at Monash University in Australia tested this hypothesis by studying land left in the wake of 2 retreating glaciers: one on an island off the coast of Antarctica and one in the Swiss Alps. The researchers sampled soils along a path from the tip of the glacier outward, which had been exposed to the air for different amounts of time. By comparing the microbial communities within these soils, the researchers could track the different stages of ecological succession after glacial retreat.
The researchers extracted DNA from the soils and analyzed it using 2 sequencing methods. First, they sequenced a gene called 16S rRNA, which is like a microbial fingerprint for the different species present. They used this method to understand the diversity of these communities and track their species overlap, helping them to identify habitat generalists that thrived under different soil conditions.
To understand the metabolic flexibility of these microbes, the researchers used a second method, known as metagenomics, which sequences all of the DNA in a sample rather than just a single gene. They used these data to reconstruct the entire genomes of microbes present in the soils, providing information on what kinds of metabolic activities they were capable of. The team also measured chemicals like ammonium and sulfide in the soils, as well as atmospheric gases like methane and carbon monoxide, to assess how the microbes used these compounds for growth.
The researchers found microbes inhabiting even the youngest soils, demonstrating the speed at which life takes hold in new environments. The abundance of microbes increased by approximately 8-fold in older soils, alongside a similar rise in species diversity, indicating that complex communities persisted over time. They also found the metabolic capabilities of microbes inhabiting Antarctic and Swiss glacial soils to be remarkably similar, suggesting common selective pressures drove the establishment of these new ecosystems.
They were surprised to discover that the most abundant microbes in younger soils were habitat specialists that were rare in older soils. These pioneer microbes, while still metabolically flexible, had adapted to utilize meager energy sources like atmospheric trace gases, including hydrogen, methane, and carbon monoxide. Many of these microbes could also derive energy from chemicals that dissolved out of rocks, like inorganic sulfur compounds. The researchers proposed that pioneer microbes could quickly take advantage of newly opened ecological niches, like soils exposed during a glacier’s retreat, because of their efficiency at using scant resources.
They found that habitat generalists, on the other hand, tended to dominate older soils. This result suggested that the habitat specialists were eventually outcompeted by the slow and steady growth of the habitat generalists in a real-life turtle-and-hare race.
The team concluded that using multiple growth strategies helps microbes adapt to new environments. However, they acknowledged that ecological succession could occur differently in other landscapes, such as in the aftermath of volcanic eruptions, meteorite impacts, or forest fires. They suggested that future researchers work to uncover how microbial communities lay the groundwork across these diverse ecosystems.
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Scientists discovered a surprising gut-heart connection that may help prevent sleep apnea from causing serious cardiovascular damage. Sleep apnea affects millions of people worldwide and is known to raise the risk of serious cardiovascular problems. Now, researchers have identified a potential new treatment target that could help reduce some of the condition’s harmful effects. Findings [...]Single cells used past nutrient shocks to change how they grew.Tea choice significantly changes kombucha’s chemistry, flavor, and antioxidant potential, with green and oolong teas showing the strongest biological activity. Kombucha has surged in popularity worldwide in recent years, but researchers are looking beyond its flavor to better understand its chemistry and possible health-related properties. A team from the Wrocław University of Environmental and Life [...]Scientists have uncovered evidence that tiny microbes living inside fish may be helping shape the chemistry of the world’s oceans. The new study, led by former graduate student Anthony Bonacolta at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, suggests that bacteria in fish intestines may work together with their hosts [...]Brown rot is a common fungal disease in the Southeastern United States that affects stone fruits like peaches, cherries, and plums. Monilinia fructicola is a tan, fuzzy fungus that grows on tree flowers, twigs, and fruit, and is the most common cause of brown rot. Once brown rot infects a tree, the damage is irreversible, causing significant crop losses in commercial orchards. Farmers try to control the spread of M. fructicola by applying chemical sprays, called fungicides, to fruit trees in the spring.
In M. fructicola, a biosynthesis gene named MfCYP51 encodes a major protein critical to the fungi’s survival. Certain fungicides, called demethylation inhibitor (DMI) fungicides, stop M. fructicola from growing by targeting this protein. Over the last 20 years, DMI fungicides have become less effective against brown rot as M. fructicola becomes more resistant.
Living microorganisms and their metabolites can control fungal diseases as an alternative to chemical fungicides, known as biofungicides. Many bacteria produce compounds like hydrogen cyanide and pyrrolnitrin that damage fungal cells. However, scientists have not found a biofungicide suitable for commercial production. A group of researchers at Clemson University in the USA and Huazhong Agricultural University in China set out to test whether the soil bacteria Pseudomonas chlororaphis and Bacillus subtilis could be effective biofungicides against brown rot.
The researchers performed an incubation experiment to analyze how the fungal cells make their critical protein from the MfCYP51 gene, a process called gene expression, under different fungicide treatments. They used 3 M. fructicola strains sensitive to traditional DMI fungicides and 3 resistant strains. They tested these with 5 different fungicide treatments: a DMI fungicide, a mixture of P. chlororaphis metabolites, a mixture of living B. subtilis cells, a DMI fungicide + P. chlororaphis metabolites, and a DMI fungicide + B. subtilis cells. They also set up a control treatment with sterile water instead of fungicide.
After 6 hours, the researchers extracted the molecule that measures gene expression, called RNA, from the fungi. They found that both the P. chlororaphis treatment and the DMI fungicide + P. chlororaphis treatment substantially reduced MfCYP51 expression in both the sensitive and resistant isolates compared to the controls. In contrast, the DMI fungicide, B. subtilis, and DMI fungicide + B. subtilis treatments increased MfCYP51 expression in the resistant isolates. The researchers concluded that P. chlororaphis has a unique ability to reduce gene expression, unlike other biofungicides.
To further investigate how the biofungicide treatments work, the team tested whether P. chlororaphis and B. subtilis produced the anti-fungal metabolite pyrrolnitrin. They added 1 milliliter of each treatment to a machine that separates and identifies liquid compounds using high pressure, called a high-performance liquid chromatograph. They found that the P. chlororaphis treatment contained pyrrolnitrin, so they hypothesized that it was responsible for reducing gene expression.
Additionally, the researchers tested their 5 treatments on brown rot in fruit. For each treatment, they took 10 Gala apples, washed and sterilized their surfaces, and sprayed them with the fungicides. After 24 hours, they poked holes in the apples with toothpicks and added 20 microliters of liquid containing M. fructicola cells to the poked holes. They placed the apples in a humid chamber for 5 days and measured the number and size of brown rot spots that developed on their surfaces.
Despite decreasing MfCYP51 expression, the researchers found that P. chlororaphis treatment alone didn’t reduce brown rot disease compared to the control, but the DMI fungicide and B. subtilis treatments did. The mixed treatments of DMI fungicide + P. chlororaphis and DMI fungicide + B. subtilis both reduced brown rot disease compared to the control, but only the DMI fungicide + P. chlororaphis treatment prevented it.
The researchers concluded that although biofungicides may not be fully effective on their own, commercializing them could allow farmers to use less DMI fungicide. They explained that scaling back the use of DMI fungicides would slow M. fructicola resistance. Finally, they proposed that future researchers test biofungicide mixtures containing pyrrolnitrin in the field to observe real-world effects on stone fruit trees.
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Scientists discovered that fog droplets can host living bacteria that grow and help remove harmful pollutants from the atmosphere, revealing fog as a surprisingly active microbial environment. Every breath you take may contain microscopic hitchhikers floating through the atmosphere. Scientists have known for years that bacteria drift through clouds and air currents, but new research [...]Greenhouse gases trap heat within the atmosphere. One such gas that exists beneath the ocean floor is methane. Ice-like substances on the seafloor that contain methane, known as methane hydrates, can break apart or melt, releasing methane gas into the ocean, risking further global warming. Melting permafrost, active tectonics, daily tidal patterns, and changing sea levels can similarly trigger methane’s escape from sediments. However, scientists don’t understand how these triggers will respond to future climate change.
A team of researchers hypothesized that future global warming could actually accelerate methane’s escape into the ocean. To investigate this hypothesis, they focused on an ancient global warming event approximately 56 million years ago, called the Paleocene-Eocene Thermal Maximum or PETM. Arctic Ocean temperatures at times exceeded 20°C (68°F) during this event. These elevated temperatures serve as an analog for today’s rapidly warming conditions.
Once methane enters seawater, its fate is largely determined by 2 sets of biological processes. Today, 90% of methane released into the ocean from the seafloor is consumed by tiny organisms called microbes via a process known as anaerobic methane oxidation. During this process, microbes consume methane alongside sulfate, producing a solid iron-sulfur mineral, pyrite. Anaerobic methane oxidation prevents methane from escaping into the atmosphere by trapping it in minerals. In this case, the ocean becomes a reservoir, or sink, for methane.
Despite this, too much methane could overwhelm the sulfate-dependent cycle. If that occurs, a different set of microbes consumes methane alongside oxygen in a process known as aerobic methane oxidation. Aerobic methane oxidation produces carbon dioxide, a potent heat-trapping greenhouse gas that escapes from the ocean. Aerobic oxidation accounts for 10% of methane consumption in oceans today, though this could have been different in the past.
To determine how much anaerobic versus aerobic methane oxidation occurred during the PETM, the team extracted data from sediments retrieved from the Arctic Ocean floor. As sediment piles up on the seafloor, it compacts. Scientists can drill deep into the seafloor to extract a cylindrical sample, or core, of this compacted sediment.
The age of sediments in a core increases with depth. Therefore, younger sediments exist at the top of the core, and older sediments exist at the bottom. For this project, the team used a previously extracted core from the Arctic Ocean that contained sediments dating back 100 million years. They found 56-million-year-old sediments from the PETM at a depth of 386 meters, or 1,266 feet, in this core.
The researchers explained that microbes leave behind unique carbon-based molecules called organic biomarkers when they decompose. These organic biomarkers accumulate in seafloor sediments. The 2 different types of methane-consuming microbes leave behind 2 different biomarkers, one for anaerobic methane oxidation and one for aerobic methane oxidation. This team measured the amount of each biomarker in the sediment core to determine which microbes were dominant during the PETM.
The biomarker left behind from microbes performing aerobic methane oxidation is called hop(17)21-ene. The researchers noticed that the amount of hop(17)21-ene increased by a factor of 4 during the PETM. At the same time, the biomarker left behind from microbes performing anaerobic methane oxidation, called glycerol dialkyl tetraether, decreased to half. They interpreted these trends to reflect the rise of aerobic methane cycling and the shutdown of anaerobic methane cycling, respectively. They attributed this transition to the release of enough methane to overwhelm the sulfate-dependent methane cycle under warming conditions.
To estimate the amount of carbon dioxide produced by aerobic methane oxidation during the PETM, the researchers located another biomarker in the sediment core, called phytane. Phytane is produced by organisms that consume carbon dioxide during photosynthesis, and its structure preserves clues to the amount of carbon dioxide available at the time. The researchers found that during and well after the PETM, the concentration of carbon dioxide in the Arctic Ocean was 4 times greater than modern levels. They concluded that the Arctic Ocean became a prolonged source of carbon dioxide to the atmosphere, even after the PETM.
The team suggested that the uptick in aerobic methane oxidation during the PETM serves as an analog for the modern Arctic Ocean, which continues to warm rapidly in the face of modern climate change. Their results highlight how the transformation of methane into carbon dioxide poses a threat. More carbon dioxide in the atmosphere warms the air, which heats the oceans, causing more methane to escape from the seafloor and eventually be converted into additional carbon dioxide. When triggered, this feedback would continue to amplify and could become difficult to recover from.
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Rod-shaped fragments of RNA called “obelisks” were discovered in gut and mouth bacteria for the first time
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