Ecology

AbstractEradicating invasive species and maintaining their populations at acceptable densities is both costly and challenging in marine environments, primarily due to the open water connectivity between culled and non-culled areas. This research aims to evaluate the short- and long-term effects of culling invasive species, considering the invasive gastropod Drupella rugosa (Born, 1778) from the coral reefs of Koh Tao (Gulf of Thailand) as a case study. Ecological, logistical, and behavioural factors that influenced the removal efforts were identified, highlighting key components that can inform future strategies aimed at managing outbreak events. Specific objectives included: (1) estimating gastropod densities and to study the behaviour of D. rugosa on Acropora-dominated reefs; (2) assessing short-term effects of D. rugosa removal by monitoring the fate of grazed corals; (3) examining the long-term impact of culling by analysing data from a removal campaign spanning over a decade, including an evaluation of the effort in terms of time and diver involvement. The relationship between damselfish and the feeding activity of corallivorous gastropods was also investigated. A key finding of this study is that poorly planned culling is ineffective in controlling outbreaks of invasive species such as those belonging to the genus Drupella. Long-term data from culling campaigns conducted between 2010 and 2024 revealed that the number of removed specimens remained relatively constant, despite significant differences in effort. This disparity underscores the lack of strategic coordination in the implementation of removal activities. Following a critical comparison with cases reported in the literature, common issues and transferable strategies were identified and thoroughly analyzed. Directions for management were provided, with the understanding that future actions should be grounded in a thorough knowledge of the species’ ecological traits, the biotic and abiotic drivers of outbreak events, a quantitative assessment of its impact on Acropora reefs, and integration into with well-established international removal and prevention programs.

Data availability

Data available on request by contacting both the correspondent Author ([email protected]) and the New Heaven Reef Conservation Program ([email protected]).
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Download referencesAcknowledgementsWe would like to thank New Heaven Reef Conservation and above all Kirsty Magson, the program manager, for providing part of the data and making this study possible. We are also deeply grateful to all the volunteers who, over the years, have contributed to the collection of data and to the implementation of the research.FundingNo Funding.Author informationAuthors and AffiliationsNew Heaven Reef Conservation Program, 48 Moo 3, Chalok Ban Kao, Koh Tao, 84360, ThailandBaruffaldi MatildeDepartment of Life and Environmental Sciences (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche s.n.c, 60131, Ancona, ItalyBaruffaldi Matilde, Roveta Camilla, Tonolini Rosita, Pulido Mantas Torcuato & Cristina Gioia Di CamilloNational Biodiversity Future Center (NBFC), Piazza Marina 61, 90133, Palermo, ItalyRoveta Camilla, Pulido Mantas Torcuato & Cristina Gioia Di CamilloConsorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, ItalyCristina Gioia Di CamilloAuthorsBaruffaldi MatildeView author publicationsSearch author on:PubMed Google ScholarRoveta CamillaView author publicationsSearch author on:PubMed Google ScholarTonolini RositaView author publicationsSearch author on:PubMed Google ScholarPulido Mantas TorcuatoView author publicationsSearch author on:PubMed Google ScholarCristina Gioia Di CamilloView author publicationsSearch author on:PubMed Google ScholarContributionsDi Camillo CG and Baruffaldi M contributed to the study conception and design. Baruffaldi M and Di Camillo CG wrote the first draft of the paper and provided figures. Baruffaldi M and Tonolini R performed samplings and collected data. Roveta C, Baruffaldi M, Pulido Mantas T analyzed data. All authors contributed to improve and revise the manuscript.Corresponding authorCorrespondence to
Cristina Gioia Di Camillo.Ethics declarations

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KeywordsBiological invasionsRemovalMuricidaeControl of pestsSurge More

AbstractFreshwater mussels (Unionidae) depend on specific fish hosts to complete their life cycle. Glochidia, their parasitic larvae, must attach to the gills or fins of suitable fish species to metamorphose. However, non-host fish may intercept glochidia, reducing larval availability for competent hosts—a phenomenon known as the dilution effect. We investigated this mechanism in a natural population of the endangered mussel Unio crassus, focusing on the interaction between the dominating host Phoxinus phoxinus and the non-host Gobio gobio. Field surveys across three separate reaches of the Warkocz River (2015–2016) and a controlled infestation experiment demonstrated that G. gobio removes a substantial proportion of glochidia without supporting their metamorphosis. Co-occurrence analysis showed a negative relation between infestation levels of G. gobio vs. P. phoxinus, with a significant interaction modulated by U. crassus density. At low mussel densities, the impact of G. gobio on parasitic success was strongest. Gobio gobio was recorded at 90% of the known U. crassus localities in Poland, and in all of these sites it formed a dominant component of the fish assemblage. Our findings provide direct evidence of a context-dependent dilution effect and highlight the importance of fish community composition and behaviour in conservation of unionid mussels. The presence of non-host fish in habitats with low mussel abundance may undermine recruitment and increase extinction risk in fragmented populations.

Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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Download referencesAcknowledgementsThe study was supported by statutory funds of the Institute of Nature Conservation, Polish Academy of Sciences. The study was conducted on the basis of permit WNP.6401.190.2014.RN-2, granted to study a protected species (U. crassus). J.D. and K.T. holds a license for conducting electrofishing in accordance with Polish legal requirements.Author informationAuthors and AffiliationsInstitute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, Kraków, 31-120, PolandJacek Dołęga, Tadeusz A. Zając, Adam Ćmiel, Anna Lipińska, Krzysztof Tatoj & Katarzyna ZającAuthorsJacek DołęgaView author publicationsSearch author on:PubMed Google ScholarTadeusz A. ZającView author publicationsSearch author on:PubMed Google ScholarAdam ĆmielView author publicationsSearch author on:PubMed Google ScholarAnna LipińskaView author publicationsSearch author on:PubMed Google ScholarKrzysztof TatojView author publicationsSearch author on:PubMed Google ScholarKatarzyna ZającView author publicationsSearch author on:PubMed Google ScholarContributionsJ.D. and T.A.Z. conceived the idea and designed the study. A.M.Ć., J.D., A.L., K.T., K.Z. and T.A.Z. collected the data. J.D., T.A.Z. A.M.Ć., and K.Z. analysed, interpreted and visualised the data. J.D. and T.A.Z. wrote the main text of the manuscript. All authors reviewed the manuscript.Corresponding authorCorrespondence to
Tadeusz A. Zając.Ethics declarations

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The authors declare no competing interests.

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Reprints and permissionsAbout this articleCite this articleDołęga, J., Zając, T.A., Ćmiel, A. et al. Evidence for dilution effect by Gobio gobio, a dead-end host in the Unio crassus–Cyprinidae coevolutionary system.
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AbstractPteridium aquilinum is a medicinally important fern with a limited range in northern Iran, increasingly threatened by climate change. Using morphological, genetic, and environmental data, we assessed differentiation, adaptive capacity, and vulnerability across 11 populations. Factor analysis of mixed data (FAMD) identified stipe indument, pinnule shape, and pinnae number as key traits distinguishing populations. Redundancy and association analyses (RDA/CCA) revealed strong links between both morphological and genetic variation and climatic gradients, particularly temperature and humidity, indicating local adaptation. Several SCoT loci were detected as adaptive outliers. Spatial PCA showed that variation is shaped by both global and local spatial factors, forming clines and local variants. Populations varied in sensitivity and adaptive capacity; populations 2, 3, 7, and 8 exhibited the lowest adaptive indices and highest vulnerability. Connectivity modeling suggested that while some populations (e.g., 2, 4, and 6) may maintain or slightly improve connectivity, others risk isolation under future climates. Structural equation modeling (SEM) indicated a positive genetic contribution to adaptation, while differential equation modeling (DEM) predicted logistic growth with temporary instability and genetic decline in vulnerable groups. Overall, findings highlight spatially uneven adaptive responses and recommend targeted conservation through connectivity enhancement, assisted gene flow, and ex-situ preservation of adaptive genotypes.

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Download referencesAuthor informationAuthors and AffiliationsDepartment of Plant Sciences and Biotechnology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, IranMasoud Sheidai, Maedeh Alaeifar & Fahimeh KoohdarAuthorsMasoud SheidaiView author publicationsSearch author on:PubMed Google ScholarMaedeh AlaeifarView author publicationsSearch author on:PubMed Google ScholarFahimeh KoohdarView author publicationsSearch author on:PubMed Google ScholarContributionsM. Sh. and F. K. Conceptualization of the project, designed the research, analysis and wrote the manuscript and M. A. collected the samples and lab work. All authors reviewed the manuscript.Corresponding authorCorrespondence to
Masoud Sheidai.Ethics declarations

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Reprints and permissionsAbout this articleCite this articleSheidai, M., Alaeifar, M. & Koohdar, F. Computational analysis and modeling of climate impact on Pteridium aquilinum (L.) populations.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-33035-1Download citationReceived: 24 August 2025Accepted: 15 December 2025Published: 19 December 2025DOI: https://doi.org/10.1038/s41598-025-33035-1Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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KeywordsMultivariate statisticsStatistical modellingSCoT markersMorphometricGenetic markers More

Abstract

Nitrogen (N) fertilization improves crop productivity. However, the long-term effects of N application on methane (CH4) emissions in drained peat soils, particularly under different hydrological conditions, remain poorly understood. Accurate quantification of CH4 emissions from peatlands is essential for assessing carbon losses and formulating effective climate change mitigation strategies. This study was conducted to investigate the impact of N fertilization on CH4 emissions and identify the main factors influencing CH4 emissions from drained tropical peatlands. This study was conducted on an oil palm plantation in Sarawak, Malaysia, a randomized block design included four N fertilizer treatments: Control (0 kg N ha− 1 yr− 1) (T1); low (31.1 kg N ha⁻¹ yr⁻¹) (T2), moderate (62.2 kg N ha⁻¹ yr⁻¹) (T3), and high (124.3 kg N ha⁻¹ yr⁻¹) (T4). Soil CH4 fluxes showed no statistically significant differences between treatments or across years, with emissions ranging from − 163.6 to 320.7 µg C m− 2 hr− 1 at T1, -86.7 to 285.8 µg C m− 2 hr− 1 at T2, -131.6 to 274.1 µg C m− 2 hr− 1 at T3 and − 125.7 to 185.9 µg C m− 2 hr− 1 at T4 (p > 0.05). Although ammonium sulfate fertilization did not significantly alter CH4 emissions, its pronounced acidifying effect on soil pH, particularly at application rates above 62.2 kg N ha⁻¹ yr⁻¹ along with elevated sulfate (SO42−) inputs and nitrogen pools exceeding the critical threshold (> 400 ppm), likely suppressed methanogenic activity and constrained soil organic matter decomposition. Water-filled pore space (WFPS) influenced CH4 emissions more than groundwater level (GWL), with the low GWL at the site limiting its impact. Increased WFPS (60–80%) reduced nitrate (NO3−) through enhanced denitrification, lowering its inhibition on CH4 production and thus increasing emissions. This study highlights the key role of soil moisture and nitrogen cycling in regulating CH4 emissions in peatland.

Data availability

The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request.
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Download referencesAcknowledgementsWe would like to express our sincere gratitude for the generous support from the Sarawak State Government and the Federal Government of Malaysia for making this research possible. We would also like to express our sincere appreciation to the dedicated staff of the Sarawak Tropical Peat Research Institute (TROPI) for their invaluable technical assistance and unwavering support throughout every phase of this study, including the challenging fieldwork. Their expertise and dedication contributed greatly to the successful completion of this study.FundingThis research was funded by the Federal Government of Malaysia and the Sarawak State Government.Author informationAuthors and AffiliationsSarawak Tropical Peat Research Institute, Kuching-Samarahan Expressway, Kota Samarahan, Sarawak, 94300, MalaysiaAuldry Chaddy, Faustina Elfrida Sangok, Sharon Yu Ling Lau & Lulie MellingAuthorsAuldry ChaddyView author publicationsSearch author on:PubMed Google ScholarFaustina Elfrida SangokView author publicationsSearch author on:PubMed Google ScholarSharon Yu Ling LauView author publicationsSearch author on:PubMed Google ScholarLulie MellingView author publicationsSearch author on:PubMed Google ScholarContributionsLiterature collection, data collection and analysis were performed by Auldry Chaddy, Faustina Elfrida Sangok, and Sharon Yu Ling Lau. The first draft of the manuscript was written by Auldry Chaddy. Faustina Elfrida Sangok, Sharon Lau Yu Ling and Lulie Melling revised the draft. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.Corresponding authorCorrespondence to
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AbstractGlobal food production requires a major upheaval to feed a burgeoning human population despite multiple disruptors, ranging from climate change to geopolitical instability. Innovation and a policy shift that focuses on the Bioeconomy could address these challenges. This Perspective highlights plant cellular agriculture, molecular farming, and plant cell culture as a potential “fourth pillar” that could diversify supply and produce high-value compounds associated with regulatory uncertainty, cost, and energy constraints.

IntroductionEvery person deserves appropriate nutrition. Our world approaches a human population of 10 billion within the next 30 years, with global food demand increasing by more than 50% during this time period1.By 2050, global food demand is projected to increase by 50–60% compared to 2010 levels, with protein demand expected to double in some regions2. This growing demand encompasses diverse nutritional needs, including high-energy staples such as rice, wheat, and maize to ensure calorie sufficiency; high-quality proteins from sources like meat, dairy, plant-based alternatives, and novel proteins to support nutrition security3; and high-value foods such as functional ingredients and specialty crops that contribute to economic diversification. Global food systems are undergoing an upheaval, with vulnerabilities such as economic shocks due to tariff changes, the risk of zoonotic infectious diseases such as bovine influenza in the US, and geopolitical conflict such as grain shortages due to the Russian- Ukraine war. Collectively, these disruptions have greatly affected food prices and availability4. However, scaling up supply across these categories is challenged by the impacts of climate change, dietary shifts driven by urbanization and rising affluence, as well as policy and trade uncertainties5.In response, and due to concerns about global food security issues, many nations such as the US are trying to change the way they produce food, to mitigate global shocks of all nature, and to decentralize yet strengthen food supply chains to reduce their vulnerabilities6. The most noteworthy way this is taking place is by investing in novel strategies to produce alternative proteins. Alternative proteins, then, refer to those made that are equally as nutritious as conventional animal proteins, but are cheaper, require fewer inputs, have a lower carbon footprint, and are resilient to climate shocks7.Alternative protein production should reduce the load of zoonotic diseases as well as agricultural pest pressures and other exacerbating problems associated with livestock production, ranging from antimicrobial resistance to animal cruelty, from fair trade to bioterrorism8. Decentralizing our food production to an abundance of smaller locations would mitigate these problems substantially. The overall effect will be a shift in trade relations from one that is fixed due to geography, to one that is fluid and unconstrained.Alternative protein technologies for food are often placed into three main categories: cultivated meat, plant-based protein, and precision fermentation9. Cultivated, or cell-based meat, refers to the production of meat cells in culture to produce a food product such as hamburger, sausage or chicken nuggets. Plant-based proteins can be defined as proteins which have been processed in such a way that they resemble animal sourced products, such as oat milk. Precision fermentation covers the use of microbial fermentation systems to produce individual animal protein in a manner that more closely resembles the technology used in the past to produce pharmaceutical proteins. This synthetic biology approach includes the incorporation of a gene encoding an animal protein into the genome of a bacterial or fungal strain, which is then cultivated in a bioreactor to produce large amounts of target proteins, such as casein and whey. These three pillars represent the fundamentals of alternative protein production.A fourth ‘pillar’ has been defined as a facet of cellular agriculture based on plant molecular farming and plant cell culture technologies. Plant molecular farming refers to the use of plants themselves to replace microbial bioreactors, in such a way that a gene of interest is expressed and extracted from plants instead of from microbes10. Plant cellular agriculture, on the other hand, makes use of plant cell culture to produce large amounts of plant biomass which can be processed into food products, analogous to some of the cultivated meat production technologies11. Plant molecular farming and plant cell culture have been proposed as a potential “fourth pillar” of alternative proteins, though their precise definition and boundaries remain debated within the field.The following Perspective presents various examples of this fourth pillar of alternative plant cell-based technologies and describes the advantages that it has over the others. The Perspective concludes with a prediction of the prospects of plant cellular agriculture to address the widening cracks found within our current food system.Plant molecular farmingPlant molecular farming can be defined as the use of plants as a production platform to express a target protein12. Originally a production platform for pharmaceutical proteins (molecular pharming) that was developed over a quarter of a century ago, the technology has matured to such an extent that animal food proteins found in dairy, meat and eggs have become a more recent series of products under development. A great advantage of plant molecular farming is that in place of costly bioreactors, greenhouses or farm fields can be used to produce the protein of interest, thus mitigating the economic and environmental costs associated with farming livestock13. Plant molecular farming thus does not encounter scaling challenges the way other protein production platforms, such as precision fermentation, must face. Plants can perform post translational modifications that more resemble their animal counterparts, thus enabling them to follow a form and functionality that is superior to proteins produced in many microbial systems14. Animal proteins can be produced and stored in a wide diversity of plant tissues, such as potato tubers, rice grains, and legumes such as peas and soybeans15. Since these are edible tissues, it is feasible that partial purification of the protein in question may be sufficient, or, depending on the circumstances, completely unnecessary. Originally, this technology was adapted by companies such as Medicago, iBio and Kentucky Bioprocessing Co, to produce vaccines, monoclonal antibodies and other biologics16. Today, over 30 molecular farming companies can be found which produce different animal food proteins. Examples include Argentinian company Moolec (recently merged with Bioceres group limited), which produces the heme protein myoglobin in soybean and pea that can be processed into iron loaded products such as textured vegetable protein (valorasoy.com). Alpine Bio (formally Nobell Foods), based in San Francisco produces dairy proteins such as casein for cheese in soybean (alpbio.com). PoloPo is an Israeli company which produces the egg protein ovalbumin in potato tubers (PoLopo.tech). In Europe, molecular farming company Nambawan Spain produces and purifies sweet proteins such as thaumatin in transgenic tobacco seed (namba-wan.com).The key steps to plant molecular farming include determining the appropriate mode of animal gene delivery to crops, then optimizing expression levels, scaling-up to produce the desired amount of protein and finally, purification of protein, if required. Animal genes can be introduced via stable transformation to produce transgenic plants, or transiently, using replicating constructs based on virus expression vectors17. To date, largely transgenic plants have been created which express the target protein; these crops can be produced in the field or greenhouse and the protein extracted using standard agricultural techniques. Limitations for these processes include regulatory issues for GMOs (for plants grown in the open field) and scale up limitations (for plants grown in the greenhouse). Transient expression performed in the greenhouse using virus expression vectors can increase yield considerably and can be introduced to field crops using novel spray technologies, which are currently under development18.Expression levels can vary depending on the type of protein being produced (this problem exists for precision fermentation as well) and the tissue that it is expressed in, as well as environmental factors such as temperature and humidity. Oilseed crops, like soy, for example, have been shown to express myoglobin at 26.6% of the total soluble protein in the legume19; this can be easily stored at ambient temperatures and extracted later, whereas the level of protein expressed in a leafy crop like lettuce or tobacco may be considerably lower, but may not require extensive purification, depending on its future use. Existing agricultural infrastructure can be used whether the plants are produced in the greenhouse or in open field, and both farming practices can support local rural economies in a fashion that is more environmentally sustainable than livestock agriculture10.A comparison between plant molecular farming and precision fermentation indicates that on average, plant molecular farming requires a much lower initial investment, Capex and scaleup costs than precision fermentation. Precision fermentation, on the other hand, has lower land use requirements but also relies on sugar and other carbon sources, as well as continuous power to run the bioreactors13. These limitations make it more challenging to scale up to global demand, due to the inhibitory costs of bioreactors and in fact sufficient access to global steel to produce them20. While transgenic plants in the open field remain subject to GMO concerns (although protein purified from such sources is not considered to be a GMO), plants do not harbor mammalian pathogens and thus contain lower safety concerns than some microbial expression systems.Artificial intelligence (AI) and machine learning (ML) are now accelerating breakthroughs in plant molecular farming by enabling high-throughput strain optimization, metabolic pathway prediction, and the identification of gene-editing targets21,22. AI-driven algorithms are increasingly used to analyze large-scale omics datasets, predict optimal gene regulatory networks, and guide the design of synthetic constructs for enhanced metabolite production23. For instance, deep learning frameworks can assist in optimizing codon usage, protein folding stability, and promoter strength for cell factory development in plants or plant cells. When combined with CRISPR-based genome editing, these tools can significantly reduce the trial-and-error cycle in engineering high-yielding production strains, paving the way for scalable and cost-effective plant-based biofactories. Integrating AI into strain design thus not only enhances precision and efficiency but also supports predictive modeling for sustainable and economically viable molecular farming systems24.Plant cell-based productsCellular agriculture, a rising field focused on producing a plant-based product directly from a single cell rather than using whole organisms in their natural habitat, offers a transformative approach for the sustainable production of ingredients used in food, cosmetics, and nutraceuticals11. Within this framework, plant cell culture serves as a powerful platform for generating high-value bioactive compounds, flavors, pigments, and even staple ingredients through controlled, in vitro methods. Techniques such as micropropagation, adventitious shoot or root formation, and somatic embryogenesis are widely applied for the regeneration of whole plants and the production of targeted compounds from cultured cells25. The commercialization of these processes using bioreactor systems helps overcome major limitations of conventional methods, which are often labor-intensive and difficult to scale. Bioreactors enable precise control of physical and chemical conditions, improve nutrient distribution, reduce physiological disorders such as hyperhydricity, and support automation, making large-scale production more efficient and economically viable26.Thus, plant-based cellular agriculture not only reduces reliance on land, water, and traditional farming practices, but also supports global efforts toward a circular and sustainable bioeconomy, where biologically derived, renewable resources drive industrial innovation, environmental sustainability, and inclusive economic growth27.Plant tissue culture involves the sterile cultivation of plant parts under controlled conditions, first conceptualized by Gottlieb Haberlandt in 1902, and based on his pioneering work with single-cell cultures28. Initially developed at the beginning of the 20th Century, plant tissue culture has come a long way since then, and includes technologies that make use of root cultures, embryonic cultures, and many others29. Plant cell culture can assist in the production of a plethora of secondary metabolites, and their yields can be vastly improved using genome editing technologies for an increasing number of plant species30. Resembling a cross between cell-based meat and precision fermentation in terms of technology, plant cell culture will facilitate the production of ingredients which would reduce supply chain disruptions. Today, plant cell culture can be produced in bioreactors as great as 100,000 L31.The number of food products that can be produced in plant cell culture has exploded and will continue to expand as concerns about supply chain disruptions grow. For example, cocoa production in cell culture is now being explored as a viable option by several different cellular agriculture companies. Current cocoa production is restricted to tropical regions and is under pressure in terms of loss of land, human rights issues, pest pressures, and is not particularly environmentally friendly32. While these issues, when combined with predictive models of climate change, will undoubtedly reduce our future global cocoa supplies, the demand for cocoa is increasing at a rate that cannot be met using traditional manufacturing processes.Plant cell culture technology is emerging as a transformative platform for the sustainable production of high-value food ingredients. Cultivation of specific plant tissues or cells in a controlled system bypasses traditional agricultural constraints such as seasonal variation, climate vulnerability, and ethical concerns related to labor practices.A notable example is California Cultured (cacultured.com), a U.S.-based biotechnology company that is producing cocoa from cell cultures. Cocoa bean cell cultivation, rapid cell growth and maturation are all possible as well as scalable. This method also minimizes the use of water and labor. It avoids environmental and social issues commonly associated with cocoa farming in West Africa, where most global cocoa is sourced.Due to increasing cocoa demand and the vulnerability of the supply chain, cell culture-based cocoa offers a scalable and ethical alternative, providing substantial reductions in land use, water consumption, and labor requirements compared to conventional cultivation. To truly understand whether plant-based or cell-culture cocoa is more sustainable, the industry needs to apply life-cycle assessment (LCA) more widely. Future LCA studies on chocolate should clearly define their system boundaries, select functional units that are relevant to the purpose, and, where possible, combine both established and newer assessment methods. Adding steps such as uncertainty and sensitivity analysis can help ensure that the results are not only accurate but also reliable for guiding decisions33.Beyond cocoa, similar cellular agriculture technologies are also being applied to coffee production. Arabica coffee is the most widely consumed variety, and is threatened by climate-induced stress and fungal pathogens34. Pluri Biotech (pluri-biotech.com), an Israeli company, is developing coffee from plant cell cultures. Using bioreactors designed to support structured cell growth, the company cultivates coffee cells capable of synthesizing key bioactive compounds such as caffeine. The resulting biomass is harvested, dried, and roasted, yielding a product that visually and sensorial resembles conventional ground coffee.In Europe, the French startup Stem (s-tem.fr) is also working with coffee cell cultures. The cultured coffee powder with natural flavor extracts derived from coffee processing byproducts creates a final product that maintains the sensory characteristics of traditionally harvested beans35.Like cocoa and coffee, cellular agriculture is now an attractive alternative for the production of other bioactive and commercially valuable compounds, including vanillin, saffron, natural colorants, flavor compounds, and dietary supplements30. Growing consumer demand for traceable, sustainable and ethically produced food sources worldwide has fueled the development of plant cell-cultured products. Plant cell culture offers a promising platform for localized, scalable, and clean-label production of essential ingredients for food, cosmetics, and nutraceuticals, addressing both environmental challenges and evolving consumer expectations. Recent advances in plant cell culture and molecular farming are driving a growing number of startups to translate the science into commercial progress. These companies illustrate the technology’s potential through measurable funding rounds, strategic partnerships, and scale-up milestones (Table 1).Table 1 Key startups in plant cell culture and molecular farming with funding and progress metricsFull size tablePlant cell culture offers reduced land use and zero exposure to pests compared to open-field agriculture; however, it requires substantial energy, high-purity water, and refined media components, including sucrose and hormones, enabling the development of heterotrophic cultures. Life-cycle assessments indicate that although emissions per biomass unit may be lower, energy consumption remains a key barrier to economic scalability without renewable energy and media recycling15,36. Techno-economic analyses further emphasize electricity and sugar sourcing as critical factors that need optimization for commercial viability37.Regulatory and ethical considerations in molecular farmingRegulatory frameworks remain a critical consideration for the deployment of products derived from plant biotechnology. While open-field genetically modified (GM) crops typically undergo approval through distinct regulatory pathways, such as the Novel Food Regulation of European Union (EU 2015/2283) and the U.S. FDA approved Generally Recognized as Safe (GRAS) process, plant cell culture–derived products from controlled environments may follow different routes with unique timelines, transparency requirements, and public consultations38. Moreover, societal concerns regarding “laboratory-grown” or “genetically modified” ingredients could impact consumer acceptance and market adoption, highlighting the importance of proactive engagement and clear communication strategies to address public perception and ethical considerations39. Specifically, the molecular farming of animal proteins in plants raises additional public health, stewardship, religious, and ethical questions, underscoring the need for collaborative dialog among scientists, regulators, industry, and religious leaders to ensure responsible development and societal acceptance40.ConclusionsThe rise of cellular agriculture and plant molecular farming has the promise to transform global food systems by producing high-quality alternative proteins and novel ingredients with reduced land and water demands. The success of this growth is hindered by the cost, scalability, consumer acceptance, technical, regulatory, and societal hurdles. Life-cycle assessments and policy frameworks can facilitate the adoption of these technologies, which can complement alternative protein, fermentation, and conventional agriculture to form a resilient and diversified landscape of plant-based products. Strategic innovation, integrating advanced breeding, AI-driven optimization, genome editing, or other breakthrough modern technologies, helps scientists select better cell lines, tweak metabolic processes, and automate production steps, along with supportive policy, to accelerate their path to scale. Combining these advances as part of sustainable food production will ensure they complement, rather than compete with, other alternative protein pillars, positioning them to play a decisive role in meeting the nutritional and environmental challenges of the coming decades for both people and the planet.

Data availability

No datasets were generated or analysed during the current study.
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Download referencesAuthor informationAuthors and AffiliationsDepartment of Microbiology, Cornell University, Ithaca, NY, USAKathleen HefferonSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY, USAAdam GannonDepartment of Biotechnology and Genetic Engineering, Jahangirnagar University, Dhaka, BangladeshAbdullah Mohammad ShohaelAuthorsKathleen HefferonView author publicationsSearch author on:PubMed Google ScholarAdam GannonView author publicationsSearch author on:PubMed Google ScholarAbdullah Mohammad ShohaelView author publicationsSearch author on:PubMed Google ScholarContributionsK.H. and A.S. wrote the main manuscript. A.G. revised and updated. All authors reviewed the manuscript.Corresponding authorCorrespondence to
Abdullah Mohammad Shohael.Ethics declarations

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Abstract

Skeletochronology combined with growth curve reconstruction is routinely used to assess the age and growth dynamics of extinct and extant vertebrates. Here we performed in vivo labelling studies of the bone histology of four 2 years-old Crocodylus niloticus individuals. We found that all the crocodiles have more growth marks in their compacta than expected for their age, i.e., they deposited stochastic growth marks in their bones. Using the fluorochrome markers we determined that these stochastic growth marks were deposited during their favourable season of growth. The variable preservation of growth marks in the crocodile bones highlights developmental plasticity in their growth, which can be extrapolated to extinct archosaurs, and other reptiles. We caution the use of growth marks in fossil bones as a reliable estimator of age and discuss the far-reaching implications this has for growth curve reconstruction and life history assessments of extinct vertebrates, such as nonavian dinosaurs.

Data availability

High resolution images will be uploaded onto Morphobank. All thin sections will be deposited in the Vertebrate Comparative Collections of Iziko Museums of Cape Town.
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Download referencesAcknowledgementsWe are grateful to Le Bonheur Reptiles and Adventures for permitting access to the crocodiles investigated here. Aurore Canoville and Andrea Plos are warmly thanked for assisting with fieldwork. Vidushi Dabee is acknowledged for having prepared some of the thin sections. We thank Viantha Naidoo and Dirk Lang at the Confocal and Light Microscope Imaging Facility of the Faculty of Health Sciences at UCT. Shafi M. Bhat of the Department of Geosciences at Auburn University, Alabama, is acknowledged for having read an earlier draft of this manuscript. Devin Hoffman and two additional anonymous reviewers are thanked for their comments. The University of Cape Town Research Committee (URC) is thanked for the postdoctoral fellowship awarded to the second author.Author informationAuthors and AffiliationsDepartment of Biological Sciences, University of Cape Town, Private Bag, Rhodes Gift, Rondebosch, 7700, South AfricaAnusuya Chinsamy & Maria-Eugenia PereyraAuthorsAnusuya ChinsamyView author publicationsSearch author on:PubMed Google ScholarMaria-Eugenia PereyraView author publicationsSearch author on:PubMed Google ScholarContributionsAC conceived and designed the project and administered the fluorochrome labelling to the crocodiles. M-EP and AC analysed the histological thin sections, and both contributed to the data interpretation and analysis.  M-EP did the confocal and petrographic micrographs and figures for the manuscript. AC wrote the first draft, and M-EP contributed to the write up and made important suggestions. Both authors approved the final version of the manuscript.Corresponding authorCorrespondence to
Anusuya Chinsamy.Ethics declarations

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The authors declare no competing interests.

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Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-022-01689-z, published online 21 March 2022.After publication of the article, an error was identified in the data entry of the maximum frequency parameter for the Suaq orangutan population. Recalculation of entropy measures and reanalysis of the mixed models revealed that, for maximum frequency, the previously reported effect of sociality is no longer statistically supported (Emergence and self-organization: F = 0.321, P = 0.573; Complexity: F = 0.009, P = 0.927). The original results for duration remain unchanged and continue to show a significant effect of sociality. While the loss of statistical support for one parameter is regrettable, the revised findings are scientifically meaningful. They align with recent findings in chimpanzees1, showing that control over vocal parameters such as frequency and duration may operate independently. This suggests that social influences on vocal phenotypes may target specific acoustic features, and that specific populations may deploy features of vocal novelty in culturally localized ways.The corrected analysis further reaffirms key methodological points raised in our original paper. In entropy-based analyses of behavioural novelty, low-probability events—sometimes mischaracterized as ‘outliers’—are not statistical noise but the core phenomena of interest. Their removal would bias entropy estimates and undermine the capacity to detect innovation. Given the nature of our study—multi-year, multi-site, and focused on a critically endangered species—each data point represents an irreplaceable behavioural observation. Removing such points without clear justification raises ethical concerns, including violation of IUCN data integrity guidelines and FAIR/TRUST data stewardship principles2,3. Our approach illustrates how ethical and methodological rigour must go hand-in-hand when working with vulnerable wild populations.For the calculation of entropy values from continuous acoustic data, equal-width binning at the individual level remains a necessary and appropriate step4. Our binning approach was selected to capture vocal originality at the level of individual phenotypes—what we term “vocal personalities”—in response to social input. Other binning choices, such as a global binning, would be unable to distinguish between individual differences and novelty; benchmarking individuals against each other would be an analysis of group conformity, not of individual originality or vocal personality.The Supplementary Information accompanying this amendment includes the original, uncorrected article for comparison (changes have been made to the Results and discussion, Methods, Table 1 and Fig. 2). Supplementary Data 3–5 have also been corrected and are available alongside the original article.The authors would like to thank Peng-Fei Fan and Zi-Di Wang for intially bringing the issue to their attention.

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Download referencesAuthor informationAuthors and AffiliationsDepartment of Psychology, University of Warwick, Coventry, UKAdriano R. LameiraSchool of Psychology and Neuroscience, University of St Andrews, St Andrews, UKAdriano R. LameiraInstituto Nacional de Electricidad y Energías Limpias, Gerencia de Tecnologías de la Información, Cuernavaca, MéxicoGuillermo Santamaría-BonfilDepartment of Life Sciences and Systems Biology, University of Torino, Turin, ItalyDeborah Galeone & Marco GambaIndependent researcher, Warwick, UKMadeleine E. HardusDepartment of Anthropology, Boston University, Boston, MA, USACheryl D. KnottBorneo Nature Foundation, Palangka Raya, IndonesiaHelen Morrogh-BernardCollege of Life and Environmental Sciences, University of Exeter, Penryn, UKHelen Morrogh-BernardThe PanEco Foundation—Sumatran Orangutan Conservation Programme, Berg am Irchel, SwitzerlandMatthew G. NowakDepartment of Anthropology, Southern Illinois University, Carbondale, IL, USAMatthew G. NowakYayasan Inisiasi Alam Rehabilitasi Indonesia, International Animal Rescue, Ketapang, IndonesiaGail Campbell-SmithSchool of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UKSerge A. WichFaculty of Science, University of Amsterdam, Amsterdam, NetherlandsSerge A. WichAuthorsAdriano R. LameiraView author publicationsSearch author on:PubMed Google ScholarGuillermo Santamaría-BonfilView author publicationsSearch author on:PubMed Google ScholarDeborah GaleoneView author publicationsSearch author on:PubMed Google ScholarMarco GambaView author publicationsSearch author on:PubMed Google ScholarMadeleine E. HardusView author publicationsSearch author on:PubMed Google ScholarCheryl D. KnottView author publicationsSearch author on:PubMed Google ScholarHelen Morrogh-BernardView author publicationsSearch author on:PubMed Google ScholarMatthew G. NowakView author publicationsSearch author on:PubMed Google ScholarGail Campbell-SmithView author publicationsSearch author on:PubMed Google ScholarSerge A. WichView author publicationsSearch author on:PubMed Google ScholarCorresponding authorCorrespondence to
Adriano R. Lameira.Supplementary informationOriginal, uncorrected articleRights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Reprints and permissionsAbout this articleCite this articleLameira, A.R., Santamaría-Bonfil, G., Galeone, D. et al. Author Correction: Sociality predicts orangutan vocal phenotype.
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AbstractFungal mitochondrial genomes are critical for understanding phylogenetics, evolution, and ecology of the Kingdom Fungi, yet they remain underrepresented in public databases. To address this, we developed a workflow to recover mitochondrial genomes from 12,902 fungal short read sequencing data housed in the Sequence Read Archive (SRA) records, assembling complete circular genomes from 2,695 species. This effort expanded fungal mitochondrial genome diversity by nearly 2.3X particularly in understudied phyla such as Mucoromycota (11X increase) and Zoopagomycota (8X increase). The new dataset contains novel yet undescribed mitochondrial genomes at numerous taxonomic levels, including 15 classes, 64 orders, 178 families, and 544 genera. Taxonomic analysis revealed broad ecological representation among the top-assembled species, including human pathogens (e.g., Cryptococcus tetragattii), plant pathogens (e.g., Melampsora larici-populina), edible mushrooms (e.g., Suillus luteus), and industrial fungi. By leveraging the not yet fully exploited SRA sequencing data, this study fills critical gaps in fungal mitochondrial genomics, tripling the currently known mitochondrial genome diversity of the Kingdom Fungi, and provides an extensive resource for phylogenetic and evolutionary research.

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Code availability

The assembly workflow was implemented in a python script (assembly_workflow.py) passing SRA run accession as input and outputting the assembly contigs and graphs, which are used by GetOrganelle for mitochondrial genome extraction (Methods). The script uses already published tools and explained in the Methods section. The script is available on GitHub at https://github.com/msabrysarhan/fungal_mtDNA.
Data availability

Nucleotide sequence data reported are available in the Third Party Annotation Section of the DDBJ/ENA/GenBank databases under the BioProject PRJNA1367877 and the accession numbers TPA: BK072095-BK074789, and the metadata is available at https://doi.org/10.6084/m9.figshare.28750034.
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Mohamed S. Sarhan.Ethics declarations

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The authors declare no competing interests.

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Reprints and permissionsAbout this articleCite this articleSarhan, M.S., Abdalrahem, A., Maixner, F. et al. De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species.
Sci Data (2025). https://doi.org/10.1038/s41597-025-06447-xDownload citationReceived: 10 April 2025Accepted: 09 December 2025Published: 18 December 2025DOI: https://doi.org/10.1038/s41597-025-06447-xShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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