Friday, August 15, 2025

 

New toolbox for breeding climate-resilient crop plants



Plant research: Publication in Nature Genetics



Heinrich-Heine University Duesseldorf

Illustration of the new analysis method 

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Illustration of the new analysis method. The tractors represent so-called transcription factors: proteins that bind to genetic switches to activate or deactivate genes. The method compares the genetic material of two parents with different traits (illustrated by the different size), within a hybrid plant. This comparison makes it possible to determine if a change in the switch sequence (orange boxes) results in stronger or weaker binding of the transcription factors, thereby altering the traits. (Fig.: HHU/Andi Kur, under licence BY-NC-SA)

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Credit: HHU/Andi Kur





An international research team headed by Heinrich Heine University Düsseldorf (HHU) and the Max Planck Institute for Plant Breeding Research in Cologne (MPIPZ) has developed a new and very precise method for identifying so-called genomic regulatory switches. These switches are responsible for the manifestation of plant traits. In the scientific journal Nature Genetics, the researchers describe that, although these regulatory switches make up only a small fraction of the genome, they can have a significant influence on plant traits. The team demonstrated the method on regulatory switches relating to drought stress, identifying promising starting points for the breeding of new maize varieties adapted to e.g. climate change.

Natural genetic variation in the genome ensures biodiversity and drives evolution. However, as natural evolutionary processes require millennia, we cannot wait for them to adapt crop plants to the rapidly changing climatic conditions, which are responsible for e.g. increased drought periods. To safeguard global food security, researchers must accelerate the identification of appropriate natural DNA variants to improve crop plant performance under stress conditions.

A research team headed by Dr Thomas Hartwig and Dr Julia Engelhorn from the Institute for Molecular Physiology at HHU and MPIPZ now presents a new, efficient method for mapping the genetic “switches” of plants in a current publication in Nature Genetics. Not actually genes themselves, these small sections of the genome determine when, where and to what extent a gene is active. They are comparable with a dimmer switch regulating the brightness of a lamp.

While research so far largely focused on the genes themselves, the new study demonstrates that key differences between plants – e.g. variation in size, or resistance to diseases or stress situations – are often not determined by the genes, but rather by these regulatory switches. Traditionally, however, it is not only difficult to locate these regions precisely, but also to determine which changes play the decisive role. This is now changing thanks to a new, scalable mapping method developed within the framework of the project.

The research team analysed 25 different maize hybrids, i.e. crossbreeds of different maize varieties, identifying over 200,000 regions in the genome where natural variations influence regulatory switches.

Dr Julia Engelhorn, lead author of the study: “Although these regulatory switches make up less than 1% of the genome, the variations often explain a substantial share of heritable trait differences – sometimes exceeding half.”

Dr Thomas Hartwig, corresponding author of the study, comments: “Understanding how these regulatory switches operate provides a powerful new tool to enhance both crop resilience and yield – laying the foundation for smarter breeding processes in the future.”

The researchers applied their method specifically to traits, which play a role in drought stress, identifying over 3,500 individual regulatory switches and the associated genes via which the plants respond to water-limited conditions.

Engelhorn: “Our approach allows direct comparison of the differences in switch variants inherited via the maternal and paternal lines in a single experiment. We can thus offer the maize research community a resource of over 3,500 drought-linked regulatory sites – opening up new possibilities to fine-tune gene expression for enhanced robustness.”

Hartwig: “The precision of this mapping enables us to learn from the natural differences in the switches how they work, which in turn enables targeted manipulation of the switches to develop plants with improved traits.”

This research was realised in collaboration with a team from the University of California in Davis, in which Dr Samantha Snodgrass is a member. The co-author of the study emphasises the change in perspective accompanying the approach: “Despite decades of successful research, much of the genome – the parts outside the genes – remains a black box. This new method pulls back the curtain and enables us to identify the function of these non-coding areas, providing biologists and breeders with new, precise targets for new research and development approaches.”

The study was conducted within the CEPLAS Cluster of Excellence on Plant Sciences at HHU and MPIPZ. Other sources of funding include the European Horizon Europe project BOOSTER, which aims to advance the development of climate-resilient cereal crops.

Original publication

Engelhorn, J., Snodgrass, S.J., Kok, A., Seetharam, A.S., Schneider, M., Kiwit, T., Singh, A., Banf, M., Khaipho-Burch, M., Runcie, D.E., Camargo, V.S., Torres-Rodriguez, J.V., Sun, G., Stam, M., Fiorani, F., Schnable, J.C., Bass, H.W., Hufford, M.B., Stich, B., Frommer, W.B., Ross-Ibarra, J., Hartwig, T. (2025). Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. Nature Genetics (2025)

DOI: 10.1038/s41588-025-02246-7

How major corn-producing regions in China achieve sustainable yield increase?




Higher Education Press
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Credit: Xiaoyu LI1 , Hongguang CAI2 , Yao LIANG2 , Shanchao YUE3 , Shiqing LI3 , Baizhao REN4 , Jiwang ZHANG4 , Wushuai ZHANG5 , Xinping CHEN5 , Qingfeng MENG6 , Peng HOU7 , Jianbo SHEN6 , Wenqi MA8 , Guozhong FENG1 , Qiang GAO1





Corn is the grain crop with the largest planting area and highest total output in China. In 2022, its planting area reached 43.1 Mha, with a total output of 277 Mt. However, the current average yield of corn in China is only 6.50 t·ha–1. Moreover, the four major producing regions—the Northeast Spring Corn Region, the North China Plain Summer Corn Region, the Northwest Spring Corn Region, and the Southwest Corn Region—face distinct yield-limiting factors due to differences in climate and soil conditions. How can we ensure food security while achieving sustainable high yields and efficiency improvement in corn production across these regions?

Recently, a research team led by Qiang Gao and Guozhong Feng from the College of Resources and Environmental Sciences at Jilin Agricultural University conducted systematic research to address this issue. By analyzing the climatic characteristics, soil physical and chemical properties, and current planting conditions of China’s major corn-producing regions, the team identified the core limiting factors for each region: black soil in the Northeast has suffered structural degradation and acidification; the North China Plain has low soil organic matter content (1.31%); the Northwest has annual precipitation of only 290 mm with severe soil desertification; and the Southwest faces challenges of high temperatures and seasonal drought. Based on these differences, the study proposed a regionalized technical model centered on integrated soil-crop system management. By optimizing planting density, nutrient management, and agronomic measures, this model synergistically improves both yield and resource use efficiency. The relevant paper has been published in Frontiers of Agricultural Science and Engineering (DOI: 10.15302/J-FASE-2025615).

This study established a “localized” technical system. For instance, to address the common issue of insufficient planting density, field experiments were conducted to determine the optimal density for each region: 67,600 plants ha–1 in the Northeast, 79,400 plants ha–1 in the North China Plain, 104,000 plants ha–1 in the Northwest, and 54,300 plants ha–1 in the Southwest. Additionally, controlled-release nitrogen fertilizer technology was introduced to synchronize nitrogen supply with crop demand, reducing nitrogen loss while increasing yields. The research also emphasized the synergistic effect of canopy light-nitrogen matching and soil organic matter improvement. For example, long-term straw returning can increase soil organic carbon by 17.7% and yield by 38.8%.

To promote the implementation of these technologies, the research team developed a “government-industry-university-research-user” collaborative promotion model. Relying on the “Science and Technology Backyard” platform, it closely connects universities, governments, cooperatives, and farmers. Taking Lishu County, Jilin Province as an example, by optimizing water and fertilizer management and moderately increasing planting density, local corn yields have significantly increased, nitrogen use efficiency has improved by 33.4%, and carbon emissions have reduced by 15%. This model not only solves the “last mile” problem in traditional technology promotion but also promotes large-scale land management.

Research results show that after the regionalized technical model is applied nationwide, the total corn output will increase by 11.5% while reducing nitrogen input by 14.7%, providing a feasible path for green agricultural development. This research provides a scientific basis for breaking the bottleneck of China’s corn production through precise matching of regional needs and technological innovation, which is of great significance for ensuring food security.

COLLECTIVE CONCIOUSNESS OF PLANTS

Densely planted maize communicates with neighboring plants to defend against pests



Summary author: Becky Ham



American Association for the Advancement of Science (AAAS)





A careful experiment by Dongsheng Guo and colleagues reveals that maize in a densely planted plot can communicate with neighboring plants through the release of the volatile gas linalool, triggering the roots of its neighbors to release compounds that can change the bacterial composition of the soil. This plant-soil communication helps the plants defend against the increased risk of pests and predation found in high-density plantings, Guo et al. conclude. The findings could aid agricultural researchers looking for ways to sustainably optimize crop yield through different planting patterns and possibly through targeting linalool production. Across several experimental plots of maize planted at different densities in China, Guo et al. noted that when concentrations of linalool in the air reach a certain plant density-dependent threshold, linalool triggers the production of jasmonate and other plant hormones in the roots of plants, which in turn leads to the release of compounds called benzoxazinoids into the soil. The benzoxazinoids alter the composition of the microbiome in surrounding soil, which helps protect the plants against pests but also leads to smaller growth. As Niklas Schandry and Claude Becker note in a related Perspective, one of the most surprising findings of the study is the speed at which this plant-soil communication happens—after only three days of maize growth at high density.

 

How plant evolution can help us fend off pests and microbes  





Michigan State University

Researcher studies mint family 

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Michigan State University biochemist Björn Hamberger is an expert in specialized metabolites known as terpenes. These compounds have long been used by humanity for their medicinal, cosmetic and flavoring properties.  

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Credit: Matthew Wisniewski/GLBRC





Fragrant garden staples part of the sprawling mint family like thyme, basil and lavender are hiding some super-sized secrets with big applications, according to Spartan researchers.    

While unraveling the genetic makeup of a mint relative called ground oak, MSU biochemists discovered it sported a truly massive genome — nearly as large as our own — as well as an extra-large gene cluster and four sets of chromosomes. 

Mint plant family members are known for their natural anti-cancer, anti-pest and anti-viral properties. Unraveling ground oak’s genetic mysteries brings researchers one step closer to reproducing these naturally powerful plant chemicals in the lab in large quantities.  

“What if we could spray our veggies with a natural product that makes a hungry deer or insect say, ‘No thank you,’” MSU researcher Björn Hamberger said, noting potential uses in large-scale agriculture.   

“These plants also have exciting antimicrobial properties, which could help with the trouble we see nowadays concerning antibiotic resistance,” he added.   

The team’s findings, which appear in the journal Plant Communications, were made possible by funding from the National Science Foundation, the National Institutes of Health, and the U.S. Department of Energy-supported Great Lakes Bioenergy Research Center.   

“This project was like many others where we walked in thinking we knew just what to do,” Hamberger said. “We’ve learned again that plants always have something more up their sleeves.”   

A family reunion    

Humans have made the most of the mint family’s dazzling chemical diversity for millennia, from medicine and fragrances to well-known culinary uses.   

At MSU, Hamberger studies these eclectic chemicals, better known as specialized metabolites — and particularly a group of molecules called terpenoids.   

Specialized metabolites are molecules that plants evolve to give them an extra edge in their environment. These are different from primary metabolites, which are the molecules a plant needs for basic survival processes like growth and reproduction.   

You might think of this molecular mix as the ingredients needed to bake a cake.    

If primary metabolites are the flour, butter and sugar that form the cake’s foundation, specialized metabolites are flavors like chocolate or vanilla that make it totally unique for each occasion.   

When a plant finds its ecological niche and inhabits it for tens of millions of years, it’ll evolve a treasure trove of specialized metabolites to adapt and thrive.    

These highly unique molecules are the sources of exciting chemical properties seen across the mint family, whether its Indian Coleus’s ability to treat glaucoma, or Texas sage, whose antimicrobial chemistry can be used against tuberculosis.    

“Plants don’t have the luxury of running away from pests or pathogens, so they turn to chemistry to get the job done,” said Hamberger, the James K. Billman Endowed Professor in the Department of Biochemistry & Molecular Biology.   

Previously, the Hamberger Lab made major breakthroughs by exploring this genetic and chemical variety.    

In 2023, his team unpacked the genome of American beautyberry, a shrub with bright magenta berries whose native chemistry repels mosquitoes and ticks. This helped shed light on how the mint family had diversified its chemistry across the ages.    

The research, which ultimately looked to synthesize compounds that could be used as cost-effective pesticides, earned Hamberger lab members Abigail Bryson and Nicholas Schlecht MSU’s Neogen Land Grant Prize.    

Awarded by my MSU’s Office of Research and Innovation, the prize highlights graduate students whose research will contribute to the scientific and economic improvement of society.   

On the hunt for further scientific surprises in the mint family, Bryson chose the understudied ground oak as the lab’s next target. Found throughout the Mediterranean basin, this mounded shrub with pinkish purple flowers earned its name for the shape of its tiny leaves. 

“We thought: let’s sequence ground oak, find out how the plants achieve their useful chemical products, and get a blueprint to build plant-derived therapeutics in the lab,” Hamberger said.   

“This was all good, until Abby found out ground oak had an unexpectedly massive surprise in store for us,” he added.   

Puzzles and clusters    

In the commonly studied plant Arabidopsis, you’ll find a modest 135 million base pairs of DNA.   

So, imagine Bryson and Hambergers’ surprise when it was revealed their ground oak contained some three billion base pairs — nearly as many as the human genome.   

To wrangle these massive genetic sums, Bryson honed her bioinformatic skills working alongside Robin Buell, a former MSU Research Foundation Professor and current Georgia Research Alliance Eminent Scholar Chair in Crop Genomics at the University of Georgia.   

“When you assemble a genome, it's like you have parts of sentences of a book, and you are trying to figure out what the story says, line by line, chapter by chapter,” Bryson said, the paper’s lead author and a current postdoctoral researcher at the Donald Danforth Plant Science Center.   

“Something about genomes that is difficult to picture is the size of the data we are working with. If the genome was the size of an actual book, the thickness of that book would be hundreds of feet, and the human and ground oak genomes would be around the size of world’s fifth tallest building,” she added.   

The group’s research efforts further benefited from Department of Plant Biology collaborators Kevin Childs and Jiming Jiang and made use of MSU’s Max T. Rogers Nuclear Magnetic Resonance facility.    

Genetic luggage    

On top of the eye-watering size of the ground oak genome, the team encountered extra surprises that helped fill in the picture of just how the mint family evolved its potent natural chemistry.    

“We found that ground oak is a tetraploid, meaning it has four copies of its genome. By comparison, we humans are diploid, so we have two — one from mom and one from dad,” Bryson said.   

“Imagine if you have to sort through and solve four puzzles dumped into the same box — that’s what Abby achieved,” Hamberger added, noting the challenges of sequencing such a complex genetic landscape.    

There was also the revelation that ground oak contained an incredibly large gene cluster. This is a genomic region where genes with similar functions are located close together.   

The Hamberger Lab found a similar, smaller cluster in their earlier study of American beautyberry, leading them to believe this cluster is evolving dynamically across many mint family plants.   

But why double or group up your genes in the first place? Hamberger says it comes down to plain old evolutionary efficiency.    

If one set of genetic information is already performing an important duty, its duplicate is free to evolve newer functions.    
 
As for having similar genes grouped together, Hamberger compares it to having your checked luggage reach the correct destination after multiple flights.     

“Once materials are packed together tightly, it’s easier to move them onto the next generation,” he explained.     

With these latest findings, the Spartan biochemists are taking the next step toward reproducing powerful, naturally occurring molecules in the lab in useable quantities.    

So, the next time you encounter a mint relative on your table or in the garden — whether it’s oregano, rosemary or even catnip — remember you’re looking at a plant whose chemistry could help us take on the world’s grand challenges.   

  By Connor Yeck  

 

In disaster-prone Nepal, farmers sticking with agriculture amid climate risks






Penn State






UNIVERSITY PARK, Pa. — For small-scale farmers up against floods, droughts and other dramatic climate events, diversifying income sources can mean financial safety — a lifeline as crop-growing conditions destabilize. But in Nepal, where natural hazards rank among the most severe in the world, how farmers perceive climate-related risks often leads them to double down on agriculture instead of exploring other livelihoods, according to a study led by a Penn State researcher.

These households may see greater risks of poverty, the research group reported in the journal Population and Environment. The findings underscore the urgency for both government and nongovernment organizations to provide crop growers globally with practical information about the climate, adaptation and alternative sources of income, the research team said.

“In a lot of places in the world, small-scale farmers are the backbone of the local food supply,” said lead author Nicolas Choquette-Levy, an assistant professor of geosciences and a faculty associate in the Earth and Environmental Systems Institute at Penn State. “Many of these farmers do it out of love. Many believe they don’t have other options for making a living, so it’s important to provide farmers with the resources to explore other options when climate makes farming less viable.”

Understanding perspective from the field is especially key for public policy, said Dirgha Jibi Ghimire, a research professor with the Population Studies Center at the University of Michigan and a study co-author.

“Insights into how smallholder farmers perceive climate-related disaster risk — and adapt their livelihoods — provide essential guidance for policymakers and development partners,” said Ghimire, who is executive director at the Institute for Social and Environmental Research – Nepal (ISER-N) in Chitwan, Nepal. “This knowledge can inform effective interventions that mitigate disaster impacts in low-income agricultural regions worldwide.”

Choquette-Levy began the study as a doctoral student at Princeton University, developing a survey of about 500 farming households in Nepal’s Chitwan Valley. Growers in the subsistence-agriculture-dependent region are among an estimated 500 million small-scale farmers worldwide, many expected to face climate-related hazards over the coming decades, according to the study.

“Whether and how small-scale agricultural communities adapt to increasing climate extremes will influence food security, natural preservation, urban migration and overall development patterns,” said Michael Oppenheimer, director of the Center for Policy Research on Energy and the Environment at Princeton University and a study co-author. “While governments have tried to make farms more resilient through education and financial investments, current efforts are insufficient to promote the widespread adaptation to a more hazardous climate.”

Agriculture accounted for 64% of Nepal’s employment and about 21% of its gross domestic product as of 2021, the researchers said.

In interviews between May and July 2022, Nepali farmers tied changing climate conditions to greater risks for their agricultural yields. The Chitwan Valley has logged roughly twice the global average temperature increase, and a drop-off in total precipitation, since 1970, according to the study. Major crops in the region include rice, maize and wheat.

At the same time, farmers believed climate-related risks in non-farming work — such as extreme heat confronting day laborers and eco-tourism workers — were even more dire, the researchers found. When farming families detect high climate risks, they may “further retrench into farming-based activities” amid climate extremes, the researchers said in the paper.

The group cited several likely factors for the pattern, including financial constraints and a fear of lost harvests. 

“People who had experienced droughts or floods ended up refocusing on farming for their income sources,” Choquette-Levy said. “Even as crop yields declined, we saw retrenchment in established farming activities. And there was very low trust in government to help farmers manage these risks.”

He returned to Nepal in summer 2025 to explore prospects for follow-up studies and to meet with policymakers about the research, reviewing results as authorities budget for public investments. In the paper, Choquette-Levy and his co-authors offered specific policy suggestions, including expanded access to climate information and financial resources for low-income farmers. Specific measures could involve subsidized crop insurance and migration assistance, they wrote.

Policymakers also ought to consider promoting “less risky opportunities” for income diversification, along with ways to spread crop-yield risks over multiple harvests, the researchers said. Meanwhile, Choquette-Levy is exploring how to apply findings from developing countries closer to home in Pennsylvania, where family farmers are navigating their own shifting conditions. Nepali farmers “are already ahead of us in approaching climate change in some ways,” he said.

“Growers in Nepal have no choice,” Choquette-Levy explained. “We cultivate some of the same crops in both parts of the world – including corn, apples and vegetables. It would be instructive to see how we can combine Nepali climate knowledge with the farming resources and entrepreneurship in Pennsylvania.”

Other contributors to the paper include Rajendra Ghimire and Dil C.K., research officer and assistant research officer, respectively, at ISER-N. 

The research also was supported by the Princeton High Meadows Environmental Institute Walbridge Fund, the Princeton Institute for International and Regional Studies, the Center for Policy Research on Energy and the Environment Nicholas Fund, and the Social Sciences and Humanities Research Council of Canada.

 

The ‘deep root’ of the Anthropocene



Impact of agricultural activities on soil erosion earlier than thought




MARUM - Center for Marine Environmental Sciences, University of Bremen

Dr. Yanming Ruan putting sample vials on the autosampler. Photo: MARUM – Center for Marine Environmental Sciences, University of Bremen; V. Diekamp 

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Dr. Yanming Ruan putting sample vials on the autosampler. Photo: MARUM – Center for Marine Environmental Sciences, University of Bremen; V. Diekamp

 

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Credit: MARUM – Center for Marine Environmental Sciences, University of Bremen; V. Diekamp





The basis for the findings of the international team, which includes researchers from Germany, the Netherlands, and China, is a sediment core obtained in 2005 during an expedition with the research vessel SONNE in the Indian Ocean off the coast of East Java (Indonesia). Particles that are transported by rain into rivers and then into the sea accumulate on the ocean floor. These samples often contain unique information about the past that is preserved in the sediments for thousands of years.

This enabled them to demonstrate how soil erosion has changed and the reasons for this. To do this, they analyzed sediments dating back to 5,000 years. For the study, the team focused on molecular markers for soil erosion and fire events and compared them with reconstructions of vegetation and hydroclimate, i.e., humidity, in this region. They divided the past 5,000 years into periods in which soil erosion changed and compared them with the other parameters to find out what the respective driving factors were. It turned out that people in this region began cultivating the land around 3,500 years ago. Without any evidence of changing vegetation or hydroclimate, fire markers increased, indicating slash-and-burn practices to clear the land. “Such early farming practices likely made soils more susceptible to erosion,” explains lead author Yanming Ruan. This is a clear signal of human influence on nature – much earlier than researchers had previously thought.

Dr. Enno Schefuß from MARUM adds: "In order to assess the influence of humans on the climate and environment, one must compare the current situation with an uninfluenced period. Our results show that we need to look back much further. In this case, we are talking about the ‘deep root of the Anthropocene’, i.e. the period in which humans have had a major impact on the natural environment and climate."

According to Ruan, the data also show that the permanent, more intensive agriculture has led to the most severe soil erosion in around 500 years. This has been exacerbated by intense monsoon rains. In the future, progressive global warming could lead to more frequent and heavier rainfall in Indonesia. According to the study's conclusion, this could further accelerate erosion rates in the future, posing risks to natural resources.

 

Original Publication:

Yanming Ruan, Mahyar Mohtadi, Lydie M. Dupont, Dierk Hebbeln, Sander van der Kaars, Wenwen Chen, Ellen C. Hopmans, Stefan Schouten, Matthias Prange, Jens Hefter, Gesine Mollenhauer, Enno Schefuß: Late Holocene human impact on tropical soil erosion in the Maritime Continent. Geophysical Research Letters 2025. DOI: 10.1029/2025GL114695 [http://dx.doi.org/10.1029/2025GL114695]

Contact:

Dr. Yanming Ruan
Organic Geochemistry
Eail: yruan@marum.de

Dr. Enno Schefuß
Molecular Paleoclimatology
Email: eschefuss@marum.de

 

Participating institutions:

  • MARUM – Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen
  • NIOZ Royal Netherlands Institute for Sea Research, Department of Microbiology and Biogeochemistry, Texel (Netherlands)
  • State Key Laboratory of Marine Geology, Tongji University (China)
  • School of Earth, Atmosphere and Environment, Monash University (Australia)
  • Cluster Earth & Climate, Department of Earth Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam (Netherlands)
  • Department of Palynology and Climate Dynamics, Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen
  • Editorial Office of Journal of Ocean University of China (China)
  • Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) Bremerhaven
  • Department of Earth Sciences, Utrecht University (Netherlands)

 

MARUM produces fundamental scientific knowledge about the role of the ocean and the ocean floor in the total Earth system. The dynamics of the ocean and the ocean floor significantly impact the entire Earth system through the interaction of geological, physical, biological and chemical processes. These influence both the climate and the global carbon cycle, and create unique biological systems. MARUM is committed to fundamental and unbiased research in the interests of society and the marine environment, and in accordance with the Sustainable Development Goals of the United Nations. It publishes its quality-assured scientific data and makes it publicly available. MARUM informs the public about new discoveries in the marine environment and provides practical knowledge through its dialogue with society. MARUM cooperates with commercial and industrial partners in accordance with its goal of protecting the marine environment.