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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In March 2021, the carcasses of at least 260 marine organisms from 81 species, including large animals called megafauna, washed ashore in South Africa. Scientists questioned whether this event was the result of an extreme temperature drop that can happen when deep, cold water rises to the surface along coastlines. Scientists refer to these rapid cooling events as coastal upwelling.
Climate change is making oceans warmer, but it’s also making coastal upwelling stronger, with unknown consequences for marine megafauna. Scientists recently studied 2 boundary currents that are rapidly warming and creating strong upwelling near the edges of sharks’ geographic ranges: the Agulhas Current in southern Africa and the East Australian Current in eastern Australia. They wanted to determine whether climate-driven changes in upwelling zones are making cold-shock events more frequent and intense, and how these events are pushing sharks beyond their temperature limits.
First, the researchers analyzed sea surface temperature data from satellites to see if rapid cooling from upwelling caused the mass marine die-off in 2021. They also obtained hourly temperature recordings from temperature loggers to measure subsurface temperature changes during the event. They found that during the March 2021 event, sea surface temperatures along the coast dropped by up to 7°C (12°F) in less than 48 hours, from 24°C (75°F) to below 17°C (63°F). Subsurface temperatures dropped faster, by more than 9°C (16°F) in 24 hours, from 21°C (70°F) to 12°C (54°F).
Bullsharks experience physiological stress at temperatures below 19°C (66°F), which is near their lower thermal limit, when migrating through rapid cooling zones. Therefore, the researchers deduced that during the 2021 cold-shock event, the sharks were exposed to temperatures several degrees below their thermal limit, possibly more than 5°C (or 10°F) colder.
The researchers also tagged 66 bull sharks with acoustic and satellite transmitters – including 41 at the Agulhas Current in South Africa and 25 at the East Australian Current in eastern Australia – to determine how they responded near their lower thermal limits in these zones. The acoustic tags record when sharks pass underwater receivers, providing information on their movements, locations, and water depths at those specific locations. In contrast, satellite tags continuously record the water temperatures and depths the sharks experience over time.
The researchers used these data to compare sharks living in warm subtropical waters with those living in cooler waters at the edge of their temperature range. The researchers found that low temperatures that persisted for long periods prevented the sharks and other megafauna from physiologically recovering. They saw that some sharks try to swim to shallower depths and look for warmer water, but cooling sometimes happened faster than they could respond.
The researchers also obtained wind records from the South African Weather Service to determine if upwelling-favorable winds happened before the 2021 event. They reported strong easterly winds pushing cold water on the surface along the coastline immediately before the event occurred. Because the cooling, strong winds, and animal deaths happened at the same time and place, the researchers inferred that upwelling was the main reason for the die-off.
Finally, the researchers examined 41 years of sea surface temperature data and used mathematical models to compute changes in the frequency and intensity of these events. Their analysis showed that rapid cooling events linked to upwelling can last a lot longer than the usual 1 to 3 days. For example, the March 2021 event lasted for 7 days.
They found that these events have increased in both frequency and intensity in the past decades, and produce more extreme temperature drops than typically happen within 24 hours. Their results suggested that the 2021 die-off was part of an increasing trend, where warming oceans allow species to move into different areas, but intense upwelling can suddenly expose them to fatal cold events. This pattern is what scientists call a climate bait-and-switch.
The researchers concluded that climate change is making coastal upwelling stronger, which can push marine megafauna beyond their thermal limits, even when initial warming appears to be beneficial. Their findings highlight an understudied aspect of climate change in the context of how temperature and upwelling cause shifts in species survival. They concluded their findings could help predict how marine ecosystems respond to future changing ocean conditions.
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For millennia, farming in Switzerland did not reduce plant diversity but helped increase it, researchers have shown in a detailed reconstruction covering the past 7000 years. Only recent decades paint a different picture.
The fall of the Roman Empire and major plague outbreaks: These events not only affected people but also reduced plant diversity on the Swiss Plateau, as human land use temporarily declined. Researchers led by Dr. Fabian Rey and Professor Oliver Heiri at the University of Basel report 1.
Their analyses are based on sediment deposits in three Swiss lakes: Moossee near Bern, Burgäschisee near Herzogenbuchsee, and Hüttwilersee in Thurgau. The researchers extracted sediment cores from these lakes and then analyzed the material deposited in the sediments over the course of millennia. This allowed them to infer and date variations in both plant diversity and agricultural land use in the areas surrounding the lakes.
“This is an exceptionally comprehensive and precisely dated dataset,” says Oliver Heiri. “It allows us to reconstruct changes in plant diversity around the lakes over the past 7000 years at a time resolution comparable to long-term ecosystem studies in modern ecology – and for a period long before modern ecology existed.”
Since the Neolithic period, plant diversity increased with increasing agricultural activity. “You might think that human impact must be bad for plant diversity, because that’s what we see today,” says Fabian Rey. “But agriculture back then made the landscape more diverse.” Before early agricultural activities, the Swiss Plateau was largely covered by forest and was therefore a relatively uniform ecosystem.
“As agriculture expanded, a mosaic of habitats emerged over time,” says Rey. Fields, pastures, hedgerows, and later orchards of tall fruit trees alternated across relatively small areas. This provided varied conditions for plants adapted to those specific environments.
However, there were also recurring periods when plant diversity declined sharply: For example, during the Migration Period following the fall of the Roman Empire, or when plague outbreaks claimed many lives in the Middle Ages. “In times when people were less able to continue farming, the forest grew back and plant diversity declined at the landscape level,” explains Heiri.
More agriculture, more biodiversity: However, this parallel trend lasted only until around World War II. Over the past 80 years, plant diversity has declined sharply. The research team attributes this to the intensification of agriculture since then.
Instead of a fragmented mosaic of habitats, large, uniform areas have emerged that are easier to farm using heavy machinery. The increasing use of fertilizers and pesticides also caused many specialized plant species to retreat.
“However, our data also show that plant diversity has recovered from earlier declines when people returned to farming practices that included varied landscapes,” says Rey. This suggests that the trend of the past 80 years could also be reversed if farming practices change again.
The data for the study are based on more than a decade of analyses of sediment cores, conducted in close collaboration with researchers from the University of Bern and the Department of Archaeology of Canton Thurgau. To collect the data, Fabian Rey extracted pollen samples from every centimeter of the cores, which he chemically processed, prepared, and analyzed under a microscope. For each sample, he identified 500 pollen grains, enabling him to determine the diversity of plants around the lake.
The intensity of agricultural use during each period was determined based on the presence of specific pollen in the samples – including both cultivated plants and species that thrive on farmland – as well as a comparison with archaeological and historical data.
The scientists dated the layers using the 14C method, a technique for determining the age of organic material. The sediment cores date back approximately 7000 years, to the Neolithic period.
 
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