@article {pmid41129320,
year = {2025},
author = {Thoms, D and Chen, MY and Liu, Y and Fulton, L and Luo, Y and Hiott, DE and Song, S and Morales Moreira, Z and Wang, NR and Zorio, D and Rejzek, M and Potter, R and Carella, P and Haney, CH},
title = {A bacterial exotoxin-triggered plant immune response restricts pathogen growth.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116457},
doi = {10.1016/j.celrep.2025.116457},
pmid = {41129320},
issn = {2211-1247},
abstract = {For optimal growth and development, hosts must promote healthy symbiotic interactions while restricting pathogens. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant root-associated strains within the Pseudomonas fluorescens species complex. Despite having similar immunogenic microbe-associated molecular patterns, one strain is beneficial and the other exhibits exotoxin-dependent virulence. We show that the two strains co-exist in vitro, but the beneficial strain outcompetes the pathogen in the rhizosphere. We find that plants respond to the pathogen, but not the beneficial strain, predominantly via an exotoxin-triggered defense response in roots. The purified exotoxin is sufficient to induce immunity and restrict bacterial growth in a BAK1/BKK1/CERK1-dependent manner. We show that these immune components are also required for balancing the growth between the beneficial and pathogenic strains. We conclude that plant immunity can distinguish phylogenetically similar microbes with distinct lifestyles, in part, through perception of exotoxins.},
}

@article {pmid41129090,
year = {2025},
author = {Kumar, A and Kumar, R and Singh, P and Kalaichelvan, S and Santos-Villalobos, SL and Kumar, N and Fernando, L and Kumar, R and Solanki, MK and Joshi, NC and Babalola, OO},
title = {Emerging Role of Arbuscular Mycorrhizal Fungi in Sustainable Agriculture: From Biology to Field Application.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70082},
doi = {10.1002/mbo3.70082},
pmid = {41129090},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {*Mycorrhizae/physiology/growth & development ; *Agriculture/methods ; Soil Microbiology ; Plant Roots/microbiology ; Symbiosis ; Agricultural Inoculants/physiology ; Crops, Agricultural/microbiology/growth & development ; },
abstract = {In recent years, increasing consumer demand for organic food and chemical free agricultural products has driven a shift toward microbial-based approaches, which are being adopted to replace traditional agrochemicals, used for nutrient supplementation and protection against plant pathogens. Arbuscular mycorrhizal fungi (AMF) can form symbiotic associations with up to 80% of plant roots, are widely employed as bio stimulants, biofertilizers, or biopesticides to improve agricultural productivity. Currently, a range of AMF strains are commercially produced and applied as soil inoculants to improve agricultural yields. Although the effectiveness of these inoculants depends on multiple factors, including the selection of AMF strains, choice of carrier materials and methods of application. In addition, production strategies play a critical role in determining both the concentration and the viability of the inoculum. Despite significant technological advancements, only a limited number of AMF strains have been commercially exploited as inoculants. Thus, the present review aims to briefly discuss the latest aspects of AMF biology, their functional role in abiotic and biotic stress management. Furthermore, this review paper also discusses different production strategies and highlights the challenges associated with the commercialization of AMF inoculants, including limited strain diversity, propagule viability, formulation stability, and inconsistent field performance.},
}

*Mycorrhizae/physiology/growth & development
*Agriculture/methods
Soil Microbiology
Plant Roots/microbiology
Symbiosis
Agricultural Inoculants/physiology
Crops, Agricultural/microbiology/growth & development

@article {pmid41128430,
year = {2025},
author = {Lin, Y and Luo, Z and Ye, Z and Zhong, N and Zhao, L and Zhang, L and Li, X and Chen, Z and Chen, Y},
title = {Applications, Challenges, and Prospects of Generative Artificial Intelligence Empowering Medical Education: Scoping Review.},
journal = {JMIR medical education},
volume = {11},
number = {},
pages = {e71125},
doi = {10.2196/71125},
pmid = {41128430},
issn = {2369-3762},
mesh = {*Artificial Intelligence/trends ; Humans ; *Education, Medical/methods/trends ; Generative Artificial Intelligence ; },
abstract = {BACKGROUND: Nowadays, generative artificial intelligence (GAI) drives medical education toward enhanced intelligence, personalization, and interactivity. With its vast generative abilities and diverse applications, GAI redefines how educational resources are accessed, teaching methods are implemented, and assessments are conducted.

OBJECTIVE: This study aimed to review the current applications of GAI in medical education; analyze its opportunities and challenges; identify its strengths and potential issues in educational methods, assessments, and resources; and capture GAI's rapid evolution and multidimensional applications in medical education, thereby providing a theoretical foundation for future practice.

METHODS: This scoping review used PubMed, Web of Science, and Scopus to analyze literature from January 2023 to October 2024, focusing on GAI applications in medical education. Following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines, 5991 articles were retrieved, with 1304 duplicates removed. The 2-stage screening (title or abstract and full-text review) excluded 4564 articles and a supplementary search included 8 articles, yielding 131 studies for final synthesis. We included (1) studies addressing GAI's applications, challenges, or future directions in medical education, (2) empirical research, systematic reviews, and meta-analyses, and (3) English-language articles. We excluded commentaries, editorials, viewpoints, perspectives, short reports, or communications with low levels of evidence, non-GAI technologies, and studies centered on other fields of medical education (eg, nursing). We integrated quantitative analysis of publication trends and Human Development Index (HDI) with thematic analysis of applications, technical limitations, and ethical implications.

RESULTS: Analysis of 131 articles revealed that 74.0% (n=97) originated from countries or regions with very high HDI, with the United States contributing the most (n=33); 14.5% (n=19) were from high HDI countries, 5.3% (n=7) from medium HDI countries, and 2.2% (n=3) from low HDI countries, with 3.8% (n=5) involving cross-HDI collaborations. ChatGPT was the most studied GAI model (n=119), followed by Gemini (n=22), Copilot (n=11), Claude (n=6), and LLaMA (n=4). Thematic analysis indicated that GAI applications in medical education mainly embody the diversification of educational methods, scientific evaluation of educational assessments, and dynamic optimization of educational resources. However, it also highlighted current limitations and potential future challenges, including insufficient scene adaptability, data quality and information bias, overreliance, and ethical controversies.

CONCLUSIONS: GAI application in medical education exhibits significant regional disparities in development, and model research statistics reflect researchers' certain usage preferences. GAI holds potential for empowering medical education, but widespread adoption requires overcoming complex technical and ethical challenges. Grounded in symbiotic agency theory, we advocate establishing the resource-method-assessment tripartite model, developing specialized models and constructing an integrated system of general large language models incorporating specialized ones, promoting resource sharing, refining ethical governance, and building an educational ecosystem fostering human-machine symbiosis, enabling deep tech-humanism integration and advancing medical education toward greater efficiency and human-centeredness.},
}

*Artificial Intelligence/trends
Humans
*Education, Medical/methods/trends
Generative Artificial Intelligence

@article {pmid41127834,
year = {2025},
author = {Zhong, Z and Hu, M and Yu, F and Yang, P and Li, L and Wang, J and Wang, Y},
title = {Aging Enhances the Ecotoxicological Effects of Biobased Microplastic Poly(Lactic Acid) and Its Adsorbed Tris(1-chloro-2-propyl)phosphate on Mussels.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {10},
pages = {1245-1260},
pmid = {41127834},
issn = {2833-8278},
abstract = {The biodegradable plastic poly-(lactic acid) (PLA) has been widely used to reduce plastic pollution in the environment, but PLA does not readily degrade completely and is more prone to form microplastics (MPs) and age. In this study, MP-PLA was aged by simulating the behavior of the marine environment and combined with plastic additive tris-(1-chloro-2-propyl)-phosphate (TCPP) according to their susceptibility to adsorb environmental pollutants. Mussels were the exposed subjects, and exposure concentrations of MPs and TCPP were set at 0.2 mg/L, 1 mg/L, and 0.5 μg/L, respectively. The ecotoxicity of PLA, aged-PLA, TCPP, and TCPP+aged-PLA was compared based on the result that aged-PLA could adsorb more TCPP. Biomarker assays revealed that mussels ingesting and accumulating contaminants underwent a severe oxidative (ROS) and immune stress response in the organism, with disruption of energy metabolism for energy supply, leading to apoptosis, resulting in tissue damage, and disruption of the homeostasis of the symbiotic intestinal microbiota. Comparisons showed that aging enhanced the adverse effects of PLA and ecotoxicological effects are further exacerbated by the adsorption of TCPP on aged-PLA. Therefore, with the widespread use of degradable plastics, long-term environmental impacts such as incomplete degradation and release of additives must be a concern.},
}

@article {pmid41127793,
year = {2025},
author = {Yoshikawa, A and Izumi, T and Kanki, T and Moritaki, T and Kitajima, M and Ohtsuchi, N and Kimura, T and Gou, Y and Hattori, R and Yumiba, M and Shirai, K and Mitchell, ML and Fujita, T and Yanagi, K},
title = {Mutualism on the deep-sea floor: a novel shell-forming sea anemone in symbiosis with a hermit crab.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250789},
pmid = {41127793},
issn = {2054-5703},
abstract = {Interspecific species interactions are fundamental evolutionary forces that shape the traits and adaptive strategies of biological communities. However, their diversity and dynamics in deep-sea ecosystems are poorly understood because of their inaccessibility. Here, we report and describe a newly identified species-specific, hermit crab-associated sea anemone named Paracalliactis tsukisome sp. nov. The sea anemone secretes and constructs a unique shell-like structure known as a carcinoecium, which expands the host hermit crab's living space. Stable isotope analyses (δ[13]C and δ[15]N) suggested that P. tsukisome sp. nov. consumes nutritional benefits by consuming host faeces and suspended organic particles from the surrounding environment. Three-dimensional computed tomography imaging elucidated a unidirectional attachment pattern, which was consistently positioned near the shell aperture or carcinoecium edge-a likely adaptation linked to feeding behaviour and carcinoecium formation. The host, Oncopagurus monstrosus (Alcock, 1894), substantially benefits from this association, attaining larger body sizes than other Oncopagurus species, highlighting the functional role of the carcinoecium as an effective shell enhancement in the deep-sea environment. This study provides the first quantitative evidence of mutualism in carcinoecium-forming associations, highlighting a remarkable example of deep-sea symbiosis and hypothesizing how reciprocal benefits are refined over time, fostering the evolution of carcinoecium-forming abilities and species-specific mutualistic relationships.},
}

@article {pmid41126179,
year = {2025},
author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG},
title = {A reference metagenome sequence of the lichen Cladonia rangiformis.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {319},
pmid = {41126179},
issn = {1741-7007},
support = {310030_212428//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; },
abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.

RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises ~ 22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.

CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.},
}

*Lichens/genetics/microbiology
*Metagenome
Symbiosis/genetics
*Genome, Fungal
*Ascomycota/genetics
Chlorophyta/genetics

@article {pmid40925005,
year = {2025},
author = {Belosokhov, A and Spribille, T},
title = {Making Fungal-Photobiont Symbioses in the Lab: Past, Present, and Future of the Elusive In Vitro Lichen.},
journal = {Annual review of microbiology},
volume = {79},
number = {1},
pages = {713-730},
doi = {10.1146/annurev-micro-051524-031834},
pmid = {40925005},
issn = {1545-3251},
mesh = {*Lichens/microbiology/physiology/growth & development ; *Symbiosis ; *Fungi/physiology/growth & development ; Coculture Techniques ; },
abstract = {The ability to synthesize lichen symbioses in vitro from pure cultures of transformable symbionts would be a game changer for experiments to identify the metabolic interplay that underpins the success of lichens. However, despite multiple reports of successful lichen resynthesis, no lichen lab model system exists today. We reviewed 150 years of in vitro lichen studies and found that the term resynthesis is applied to many types of fungal-photobiont cocultures that do not resemble lichens. Some of the most lichen-like results, for their part, were obtained from nonaxenic tissue culture. Only a few studies reported obtaining natural-looking lichens from axenic input cultures, but all appear to have been isolated successes obtained against the background of extensive contamination. We suggest revisiting resynthesis experiments in light of recent advances in our understanding of lichen microbial composition to test whether in vitro lichen morphogenesis requires microbial inputs beyond those of the canonical fungal and algal symbionts.},
}

*Lichens/microbiology/physiology/growth & development
*Symbiosis
*Fungi/physiology/growth & development
Coculture Techniques

@article {pmid41125883,
year = {2025},
author = {Vaga, CF and Quattrini, AM and Galvão de Lossio E Seiblitz, I and Huang, D and Quek, ZBR and Stolarski, J and Cairns, SD and Kitahara, MV},
title = {A global coral phylogeny reveals resilience and vulnerability through deep time.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41125883},
issn = {1476-4687},
abstract = {Global climate change and its consequences for the symbiosis between corals and microalgae are impacting coral reefs worldwide-ecosystems that support more than one-quarter of marine species and sustain nearly one billion people[1-3]. Understanding how stony corals, the primary architects of both shallow and deep reef ecosystems, responded to past environmental challenges is key to predicting their future[4]. Here we describe a time-calibrated molecular phylogenetic analysis that includes hundreds of newly sequenced coral taxa, and sheds light on the deep-time evolution of scleractinian corals. We date the emergence of the most recent common ancestor of Scleractinia to about 460 million years ago and infer that it was probably a solitary, heterotrophic and free-living organism-or one that could reproduce through transverse division-thriving in both shallow and deep waters. Our analyses suggest that symbiosis with photosynthetic dinoflagellates was established around 300 million years ago and spurred coral diversification. However, only a few photosymbiotic lineages survived major environmental disruptions in the Mesozoic era. By contrast, solitary, heterotrophic corals with flexible depth and substrate preferences appear to have thrived in the deep sea despite these environmental disturbance events. Even though ongoing environmental changes are expected to severely affect shallow reefs[5], our finding that stony corals have shown resilience throughout geological history offers hope for the persistence of some lineages in the face of climate and other environmental changes.},
}

@article {pmid41125850,
year = {2025},
author = {Salloum, Y and Gros, G and Quintero-Castillo, K and Garcia-Baudino, C and Rabahi, S and Janardhana Kurup, A and Diabangouaya, P and Pérez-Pascual, D and Morales Castro, RA and Boekhorst, J and Villablanca, EJ and Ghigo, JM and Feijoo, CG and Brugman, S and Hernandez, PP},
title = {IL-26 from innate lymphoid cells regulates early-life gut epithelial homeostasis by shaping microbiota composition.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41125850},
issn = {1460-2075},
support = {ANR-24-INBS-0005 FBI BIOGEN//Agence Nationale de la Recherche (ANR)/ ; ANR-II-INBS-0014//Agence Nationale de la Recherche (ANR)/ ; ANR-11- LBX-0044//Agence Nationale de la Recherche (ANR)/ ; ANR-10-IDEX- 0001-02 PSL//Agence Nationale de la Recherche (ANR)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (ANR)/ ; 2020 DAE 78//Ville da Paris Emergence Program/ ; AJE201905008718//Fondation pour la Recherche Médicale (FRM)/ ; FDT202304016654//Fondation pour la Recherche Médicale (FRM)/ ; R21045DS//ATIP-Avenir Starting Program/ ; 101041422//EC | European Research Council (ERC)/ ; },
abstract = {Animals host symbiotic microbial communities that shape gut health. However, how the host immune system and microbiota interact to regulate epithelial homeostasis, particularly during early development, remains largely unclear. Human interleukin-26 (IL-26) is associated with gut inflammation and has intrinsic bactericidal activity in vitro, yet its in vivo functions are largely unknown, primarily due to its absence in rodents. To examine the role of IL-26 in early life, we used zebrafish and found that gut epithelial cells in il26-/- larvae exhibited increased proliferation, faster turnover, elevated DNA damage, and altered cell population abundance. This epithelial dysregulation occurred independently of the IL-26 canonical receptor and resulted from dysbiosis in il26-/- larvae. Moreover, IL-26 bactericidal activity was conserved in zebrafish, suggesting a potential role of this property in regulating microbiota composition. We further identified innate lymphoid cells (ILCs) as the primary source of IL-26 at this developmental stage. These findings establish IL-26 as a central player in a regulatory circuit linking the microbiota, ILCs, and intestinal epithelial cells to maintain gut homeostasis during early life.},
}

@article {pmid41124367,
year = {2025},
author = {Oladipupo, SO and Hochstrasser, M},
title = {Deubiquitylases and nucleases in bacterial symbiont-induced cytoplasmic incompatibility.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20253047},
pmid = {41124367},
issn = {1470-8752},
abstract = {In myriad arthropod species, maternally transmitted symbiotic bacteria spread through populations by manipulating host reproduction, most frequently by a mechanism called cytoplasmic incompatibility (CI). CI occurs when bacterially infected males fertilize uninfected females, typically causing paternal chromatin condensation and segregation defects and usually embryonic arrest in the first zygotic cell cycle. Embryos survive if the female is similarly infected, which promotes bacterial spread. The endosymbiont best known for CI is Wolbachia, now widely used against mosquitoes that vector viral diseases such as dengue fever. Although CI is induced by Wolbachia resident in testes, mature sperm carry no bacteria, indicating they alter sperm in a way that, following fertilization, interferes with embryogenesis. CI-inducing factors (Cifs) are expressed from syntenic Wolbachia cifA-cifB genes. CifB is required in the male germline to induce CI, while CifA expression in the host female is sufficient to rescue viability. Importantly, CifA suppresses lethality through its binding to CifB. Different CifB proteins have distinct CI-relevant enzymatic functions, in particular, deubiquitylase and nuclease activities. Consistent with these genetic data, CifB is packaged into sperm during spermiogenesis. While sperm morphological disruption has been observed in fruit flies carrying cif transgenes, a causal role in CI is unclear. Also not understood is how maternally provisioned CifA rescues embryo viability. Exciting new findings with diverse symbiotic bacteria reveal cifA-cifB-like operons on extrachromosomal plasmids. These results suggest far wider deployment of Wolbachia-related CI factors than previously thought and multiple mechanisms for lateral cif gene transfer.},
}

@article {pmid41124138,
year = {2025},
author = {Bennett, JA and Elshamy, O and Trefiak, M and Wasan, JP},
title = {Fertilizer and fungicide reduce herbicide efficacy and enhance growth of invasive common tansy (Tanacetum vulgare).},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333818},
doi = {10.1371/journal.pone.0333818},
pmid = {41124138},
issn = {1932-6203},
mesh = {*Herbicides/pharmacology ; *Fertilizers ; *Introduced Species ; *Fungicides, Industrial/pharmacology ; *Tanacetum/growth & development/drug effects/microbiology ; Mycorrhizae/drug effects ; Biomass ; },
abstract = {Common tansy (Tanacetum vulgare; Asteraceae) is a widespread invasive species in North America that threatens biodiversity and agricultural productivity by displacing resident vegetation. Combined with being unpalatable, it can be toxic and thus poses significant challenges for the livestock industry. Current tansy control strategies are largely chemical and rely on a suite of synthetic auxin herbicides. The need for reapplication may lead to resistance development in addition to significant biodiversity losses. Recent work suggests that invasive Asteraceae may rely on symbiotic arbuscular mycorrhizal fungi (AMF) to give them a competitive advantage. We hypothesized that suppressing AMF would reduce tansy growth and reduce reliance on more damaging herbicides. Fungicides and fertilizers, known to suppress AMF, may be potential tools for tansy suppression by reducing its competitive ability; however, both may also enhance invader growth and represent a significant risk. We conducted a two-year experiment crossing three herbicides, with varying degrees of residual control, with fungicide and fertilizer treatments to explore their effects on tansy. Despite initially reducing AMF abundances, both fertilizer and fungicide unexpectedly improved tansy growth, especially when applied with the non-residual herbicide (2,4-D), where strong control was eliminated by either treatment. This suggests that, at least at our study site, any suppression of AMF did not affect tansy strongly enough to overcome the benefits of increased nutrients and pathogen suppression. Independent of fungicide or fertilizer, all three herbicides reduced tansy biomass and increased community biomass by year two, driven by increases in grasses. The most effective herbicide (picloram), however, also caused the greatest declines in broadleaf plants, leading to significant species losses. Conversely, 2,4-D was only slightly less effective after two years, while having limited non-target effects. Non-residual herbicides, like 2-4D, may offer a better balance between tansy control and biodiversity conservation.},
}

*Herbicides/pharmacology
*Fertilizers
*Introduced Species
*Fungicides, Industrial/pharmacology
*Tanacetum/growth & development/drug effects/microbiology
Mycorrhizae/drug effects
Biomass

@article {pmid41122663,
year = {2025},
author = {Huang, Z and Ren, G and Guo, X and Su, Y and Wang, Y and Zhang, S and Qi, X and Lu, H and Lian, J and Liang, Y},
title = {Cysteine-rich receptor-like secreted protein 1 promotes intercellular infection and enhances nodulation in Aeschynomene indica.},
journal = {Horticulture research},
volume = {12},
number = {10},
pages = {uhaf185},
pmid = {41122663},
issn = {2662-6810},
abstract = {Nitrogen-fixing bacteria establish symbiotic relationships with their host plants via two different entry systems: root hair-mediated (intracellular) entry and intercellular entry. However, the molecular mechanisms underlying the intercellular entry system have received relatively little research attention. In this study, we compared the transcriptomes of the nodules and roots of Myrica rubra, which forms an ancient type of symbiosis with Frankia via intercellular entry. We found that cysteine-rich receptor-like secreted protein 1 (CRRSP1) was highly upregulated in M. rubra nodules. We then investigated the function of MrCRRSP1 in Aeschynomene indica, which establishes symbiosis with Bradyrhizobium sp. ORS285 through an intercellular entry system. The overexpression of MrCRRSP1 and AiCRRSP1 in A. indica enhanced the nodule number and plant growth. Exogenous application of glutathione S-transferase (GST)-tagged MrCRRSP1 and AiCRRSP1 in A. indica promoted rhizobial attachment at cracks in the lateral root base, as well as rhizobial motility and biofilm formation. These results suggest that CRRSP1 promotes nodulation by enhancing rhizobial attachment to lateral root cracks. In addition to providing new insights into the molecular mechanisms underlying nodule formation through intercellular entry, this research enhances our understanding of actinorhizal plant-Frankia symbiosis.},
}

@article {pmid41120889,
year = {2025},
author = {Lu, BF and Kang, WJ and Shi, SL and Jing, F and Guan, J},
title = {Comparative transcriptomics reveals differential carbohydrate and lipid metabolism in roots and nodules of Rhizobia-Inoculated alfalfa (Medicago sativa L.).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1413},
pmid = {41120889},
issn = {1471-2229},
support = {No. GSAU-DKZY-2024-002//The Joint Fund for Counterpart Support Research of China Agricultural University/ ; No. GSAU-DKZY-2024-002//The Joint Fund for Counterpart Support Research of China Agricultural University/ ; No. GSAU-DKZY-2024-002//The Joint Fund for Counterpart Support Research of China Agricultural University/ ; No. GSAU-DKZY-2024-002//The Joint Fund for Counterpart Support Research of China Agricultural University/ ; No. GSAU-DKZY-2024-002//The Joint Fund for Counterpart Support Research of China Agricultural University/ ; No. KLGE-2022-01//The Open Project of Key Laboratory of Pratacultural Ecosystems of Ministry of Education (Gansu Agricultural University)/ ; No. KLGE-2022-01//The Open Project of Key Laboratory of Pratacultural Ecosystems of Ministry of Education (Gansu Agricultural University)/ ; No. KLGE-2022-01//The Open Project of Key Laboratory of Pratacultural Ecosystems of Ministry of Education (Gansu Agricultural University)/ ; No. KLGE-2022-01//The Open Project of Key Laboratory of Pratacultural Ecosystems of Ministry of Education (Gansu Agricultural University)/ ; No. KLGE-2022-01//The Open Project of Key Laboratory of Pratacultural Ecosystems of Ministry of Education (Gansu Agricultural University)/ ; },
mesh = {*Medicago sativa/metabolism/microbiology/genetics ; *Lipid Metabolism/genetics ; *Carbohydrate Metabolism/genetics ; *Root Nodules, Plant/metabolism/microbiology/genetics ; *Plant Roots/metabolism/microbiology/genetics ; *Transcriptome ; Symbiosis ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Rhizobium/physiology ; },
abstract = {BACKGROUND: The symbiotic nitrogen-fixing system formed between alfalfa (Medicago sativa L.) and rhizobia requires precise regulation of carbohydrate and lipid metabolism to sustain their high-energy-demand system. However, metabolic divergence between roots and nodules remains poorly characterized.

RESULTS: Using comparative transcriptomics, we analyzed gene expression profiles in pink nodules (PN), white nodules (WN), Pink nodule roots (PNR), white nodule roots (WNR), non-nodule roots (NNR) and control roots (CKR) from rhizobia-inoculated plants at 35 days post-inoculation. Key findings revealed metabolic specialization between tissues: PN exhibited elevated expression of lipid catabolism genes (MsECHIA, MsACX) and key genes of the TCA cycle regulators, driving direct energy supply for nitrogenase activity. PNR, WNR preferentially expressed glycolysis (MsPKP2) and pentose phosphate pathway (MsG6PD5) genes to convert photoassimilates into dicarboxylic acids via a directional transport system to nodules. WN showed enriched fatty acid elongation genes (MsKCR1, MsHACD2), suggesting compensatory synthesis of structural lipid to maintain symbiotic interfaces under carbon limitation. NNR, CKR retained starch metabolism dominance. Weighted geneco-expression network analysis revealed that symbiotic signaling synchronizes nodule lipid degradation with root carbon repartitioning to prioritize photoassimilate allocation to nodules. Nodulated roots may supplement nodule energetics through lipid precursor synthesis or storage lipid hydrolysis, thereby forming a "root-nodule metabolic relay" mechanism. Our results demonstrate that the alfalfa-rhizobia symbiosis establishes a hierarchical energy distribution network through tissue-specific regulation of metabolic genes, coordinating nitrogen fixation efficiency with energy supply homeostasis.

CONCLUSIONS: This study elucidates metabolic coordination mechanisms underlying legume-rhizobial symbiosis, providing a theoretical framework for optimizing symbiotic energy economics through targeted gene editing approaches.},
}

*Medicago sativa/metabolism/microbiology/genetics
*Lipid Metabolism/genetics
*Carbohydrate Metabolism/genetics
*Root Nodules, Plant/metabolism/microbiology/genetics
*Plant Roots/metabolism/microbiology/genetics
*Transcriptome
Symbiosis
Gene Expression Profiling
Gene Expression Regulation, Plant
*Rhizobium/physiology

@article {pmid41120066,
year = {2025},
author = {Brioukhanov, AL and Chelebieva, ES and Kladchenko, ES and Podolskaya, MS and Gavruseva, TV and Andreyeva, AY},
title = {Gill microbiome and tissue microstructural damages of the Pacific oyster Magallana gigas following the infection with boring sponge Pione vastifica.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108477},
doi = {10.1016/j.jip.2025.108477},
pmid = {41120066},
issn = {1096-0805},
abstract = {Clionid boring sponges are pests that may colonize the shells of bivalve mollusks, including Pacific oysters (Magallana gigas). Infection with the boring sponge Pione vastifica can be associated with fitness of oysters by reducing their growth rate and survival. Microbial communities play an important role in the host's ability to adapt and survive under disease, and they are extremely sensitive to invasions by pathogens and parasites. In this study, we compared the diversity of gill microbiomes in a group of Pacific oysters that were parasitized by the boring sponge (P. vastifica), and a control group of healthy oysters without signs of sponge presence on shells. In addition, we evaluated histopathological lesions in gills of sponge-infected oysters. The microstructure of gills was significantly damaged in oysters with the boring sponge settled on shells and showed numerous histological lesions including inflammation, necrosis and abnormalities of filaments. Abundant hemocyte infiltration indicated active immune response in respiratory tissue of infected oysters. Histopathological changes in gills were accompanied with the transition of the microbial community to disbalance state. The taxonomic diversity of symbiotic microorganisms in the infected oysters was significantly lower than in the healthy mollusks. The drastic changes at both higher and lower levels of taxonomic ranks of microorganisms were observed. These findings indicate that infection by boring sponges is associated with the substantial changes in gill microbiome and provide new insights into the effects of boring sponges on symbiotic bacterial communities within the Pacific oysters they inhabit.},
}

@article {pmid41119448,
year = {2025},
author = {Gallego, D and Dios, MNG and Riba-Flinch, JM and Garca-Reina, A and Galin, J and Mas, H and Lencina, JL and Zafra, M and Henares, I and Rodrguez, F and Alczar, MD and Knek, M and Gmez, DF},
title = {Euwallacea similis (Ferrari), a new ambrosia beetle (Coleoptera: Curculionidae: Scolytinae) for the Iberian Peninsula, and new records on Euwallacea fornicatus (Eichhoff), Xyleborus bispinatus Eichhoff and Amasa parviseta Knek & Smith.},
journal = {Zootaxa},
volume = {5673},
number = {1},
pages = {63-78},
doi = {10.11646/zootaxa.5673.1.4},
pmid = {41119448},
issn = {1175-5334},
mesh = {Animals ; Spain ; *Weevils/classification/anatomy & histology/growth & development/physiology ; Animal Distribution ; Male ; Female ; Introduced Species ; Ecosystem ; Animal Structures/anatomy & histology/growth & development ; Body Size ; Organ Size ; },
abstract = {The rise of invasive species is a global concern, increasingly driven by international trade and climate change. Ambrosia beetles (Xyleborini) are particularly successful invaders due to their ability of asexual reproduction and symbiotic relationship with fungi. Here we report and map the distribution of Xyleborini alien species in the Iberian Peninsula, expanding knowledge about the distribution of already established species and identifying a new host plant for Xyleborus bispinatus. Some populations have been detected through early detection trapping networks. The presence of Euwallacea fornicatus and E. similis is confirmed for the first time in the Iberian Peninsula, with E. similis establishing populations in Southeastern Spain, while E. fornicatus is confirmed in the South, affecting avocado crops. Additionally, the distribution of X. bispinatus has been expanded. Amasa parviseta was also recorded, suggesting a broader distribution than previously known. The study highlights the increasing arrival and establishment of invasive Xyleborini in Spain, likely driven by trade, climate change, and urban development. This work underscores the urgent need for monitoring and early detection programs to manage and mitigate potential impacts.},
}

Animals
Spain
*Weevils/classification/anatomy & histology/growth & development/physiology
Animal Distribution
Male
Female
Introduced Species
Ecosystem
Animal Structures/anatomy & histology/growth & development
Body Size
Organ Size

@article {pmid41119352,
year = {2025},
author = {Syomin, V and Anker, A and Kolbasova, G and Carvalho, S},
title = {Parahesione dudahamra sp. nov., an eye-catching symbiotic worm from the Red Sea, with complementary description and notes on Leocrates giardi Gravier, 1900 (Annelida: Phyllodocida: Hesionidae).},
journal = {Zootaxa},
volume = {5673},
number = {2},
pages = {189-212},
doi = {10.11646/zootaxa.5673.2.2},
pmid = {41119352},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; Male ; Female ; Symbiosis ; Saudi Arabia ; *Polychaeta/anatomy & histology/classification/physiology/growth & development ; Animal Distribution ; Body Size ; Animal Structures/growth & development/anatomy & histology ; Organ Size ; Ecosystem ; },
abstract = {A new, brightly red-coloured, symbiotic hesionid worm, Parahesione dudahamra sp. nov., is described based on the holotype and single specimen collected in the shore waters of the King Abdullah University of Science and Technology, Thuwal, Red Sea coast of Saudi Arabia. The new species is characterized by simple lateral antennae without distinct ceratophores, longest dorsal cirri reaching chaetiger 12, and longest ventral cirri reaching only chaetiger 4. The holotype was extracted from a burrow of an unknown host in very shallow water, close to mangrove roots. The diversified burrowing fauna of the type locality, including the possible infaunal hosts of P. dudahamra sp. nov., is briefly discussed. In addition, a full description and ecological notes are provided for another hesionid worm, Leocrates giardi Gravier, 1900, of which several specimens were extracted from burrows at the type locality of P. dudahamra sp. nov.},
}

Animals
Indian Ocean
Male
Female
Symbiosis
Saudi Arabia
*Polychaeta/anatomy & histology/classification/physiology/growth & development
Animal Distribution
Body Size
Animal Structures/growth & development/anatomy & histology
Organ Size
Ecosystem

@article {pmid41119268,
year = {2025},
author = {Boyko, CB and Williams, JD},
title = {New records of crustacean (Isopoda: Bopyridae and Cirripedia: Rhizocephala) and molluscan (Bivalvia: Galeommatoidea) symbionts from gebiid mud shrimps (Crustacea: Decapoda: Gebiidea) with description of a new species of Gyge Cornalia & Panceli, 1861 from Iran.},
journal = {Zootaxa},
volume = {5621},
number = {5},
pages = {571-586},
doi = {10.11646/zootaxa.5621.5.5},
pmid = {41119268},
issn = {1175-5334},
mesh = {Animals ; Male ; *Isopoda/anatomy & histology/classification/physiology/growth & development ; Female ; Symbiosis ; Animal Distribution ; Body Size ; Animal Structures/anatomy & histology/growth & development ; Organ Size ; *Bivalvia/physiology/classification/anatomy & histology ; *Decapoda/parasitology ; Ecosystem ; },
abstract = {Gebiid mud shrimps host numerous symbionts including nearly 40 described species of parasitic epicaridean isopods as well as rhizocephalan barnacles and bivalve molluscs. Collections of gebiids from the Senckenberg Forschungsinstitut were examined to locate new and previously cited specimens bearing bopyrid, rhizocephalan and mollusc symbionts. We report on material from Japan consisting of four species of bopyrid isopods from three genera (Gyge, Phyllodurus, and Procepon), one rhizocephalan barnacle (Parasacculina shiinoi), and one symbiotic bivalve (Peregrinamor ohshimai). The record of the abdominal bopyrid Phyllodurus sp. is based on a single male specimen but likely represents a new species although more material is needed to make that determination. We also report on an additional two species of Gyge: one from European waters (G. branchialis) and one new species from the Persian Gulf. The new species can be distinguished from its closest congener based on the female uropods being visible in dorsal view and having a straight posterior lobe of the first oostegite plus the male having large midventral tubercles on the posterior five pereomeres and all pleomeres. A key to females of all species of Gyge is provided.},
}

Animals
Male
*Isopoda/anatomy & histology/classification/physiology/growth & development
Female
Symbiosis
Animal Distribution
Body Size
Animal Structures/anatomy & histology/growth & development
Organ Size
*Bivalvia/physiology/classification/anatomy & histology
*Decapoda/parasitology
Ecosystem

@article {pmid41119070,
year = {2025},
author = {Nel, WJ and Duong, TA and Fell, S and Herron, DA and Paap, T and Wingfield, MJ and Beer, ZW and Hulcr, J and Johnson, AJ},
title = {A checklist of South African bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae, Platypodinae).},
journal = {Zootaxa},
volume = {5648},
number = {1},
pages = {1-101},
doi = {10.11646/zootaxa.5648.1.1},
pmid = {41119070},
issn = {1175-5334},
mesh = {Animals ; South Africa ; *Weevils/classification/anatomy & histology/growth & development ; Male ; Female ; Animal Distribution ; Checklist ; *Coleoptera/classification ; Biodiversity ; },
abstract = {The global spread of bark and ambrosia beetles (Coleoptera: Curculionidae), together with their symbiotic fungi, has become a major threat to forest health in recent years. Consequently, they have been extensively studied in many Northern Hemisphere countries where their species diversities are relatively well documented. In contrast, these insects have attracted relatively little research interest in the Southern Hemisphere. In this study we address this knowledge gap by cataloguing the bark and ambrosia beetle diversity of South Africa. More than 200 species of bark and ambrosia beetles were found to be present in the country, 16 of which are reported for the first time. This catalogue will provide a foundation for future surveys and studies on bark and ambrosia beetles not only in South Africa but also on the African continent.},
}

Animals
South Africa
*Weevils/classification/anatomy & histology/growth & development
Male
Female
Animal Distribution
Checklist
*Coleoptera/classification
Biodiversity

@article {pmid41117958,
year = {2025},
author = {Koech, N and Muoma, J and Banerjee, A and Okoth, P and Wekesa, C},
title = {Modular evolution and regulatory diversification of nodD-like LysR-type transcriptional regulators in α-Proteobacteria.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {327},
pmid = {41117958},
issn = {1432-072X},
mesh = {*Bacterial Proteins/genetics/metabolism/chemistry ; *Transcription Factors/genetics/metabolism/chemistry ; *Gene Expression Regulation, Bacterial ; *Evolution, Molecular ; *Alphaproteobacteria/genetics/classification/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Bacterial ; Operon ; Symbiosis ; },
abstract = {The nodD gene encodes a LysR-type transcriptional regulator critical for nodulation gene expression in rhizobia, yet its evolutionary origin, structural plasticity, and regulatory reach beyond symbiosis remain incompletely resolved. Here we investigate the genomic organization, structural variation, and functional diversification of nodD and its homologs across α-proteobacteria with selected outgroups. Using orthogroup-based pangenome clustering, dated species trees, and gene-tree-species-tree reconciliation, we reconstruct the evolutionary trajectory of nodD, indicating emergence from ancient LTTRs deep in proteobacterial history. Reconciliation reveals widespread duplication and horizontal gene transfer (HGT), with several rhizobia showing notable duplication and exchange, and marine/non-rhizobial taxa contributing to a mosaic of nodD-like genes. Gene-neighborhood and operon analyses show conserved syntenic tendencies in classical rhizobia but extensive architectural divergence in free-living lineages, including frequent monocistronic anchors with extended upstream regions and, when polycistronic, enrichment for transporters and local metabolic enzymes within compact multi-regulator cassettes. Structural comparisons with AlphaFold and PyMOL confirm the canonical LTTR fold while uncovering species-specific deviations concentrated in effector-binding loops and interfaces. Motif discovery and genome-wide scanning identify targets involved in metabolism, stress responses, and transcriptional control, and network analysis reveals modular connectivity spanning core metabolism and accessory processes such as secondary metabolism, transport, and biofilm-associated functions. These findings portray nodD as a structurally conserved yet functionally flexible regulator repeatedly reshaped by duplication, HGT, and local genome context, extending nodD-like systems beyond symbiosis and broadening the regulatory landscape of bacterial LTTRs.},
}

*Bacterial Proteins/genetics/metabolism/chemistry
*Transcription Factors/genetics/metabolism/chemistry
*Gene Expression Regulation, Bacterial
*Evolution, Molecular
*Alphaproteobacteria/genetics/classification/metabolism
Phylogeny
Gene Transfer, Horizontal
Genome, Bacterial
Operon
Symbiosis

@article {pmid41117506,
year = {2025},
author = {Mineo, CR and Jiang, J and Martinez-Gomez, NC},
title = {XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0130425},
doi = {10.1128/aem.01304-25},
pmid = {41117506},
issn = {1098-5336},
abstract = {Nodule-forming bacteria play crucial roles in plant health and nutrition by providing fixed nitrogen to leguminous plants. Despite the importance of this relationship, how nodule-forming bacteria are affected by plant exudates and soil minerals is not fully characterized. Here, the effects of plant-derived methanol and lanthanide metals on the growth of nitrogen-fixing Rhizobiales are examined. Prior work has demonstrated that select Bradyrhizobium strains can assimilate methanol only in the presence of lanthanide metals; however, the pathway enabling assimilation remains unknown. In this study, we characterize Bradyrhizobium diazoefficiens USDA 110, Bradyrhizobium sp. USDA 3456, and Sinorhizobium meliloti 2011 to determine the pathways involved in methanol metabolism in previously characterized strains, other clades of Bradyrhizobium, and the more distantly related Sinorhizobium. Based on genomic analyses, we hypothesized that methanol assimilation in these organisms occurs via the lanthanide-dependent methanol dehydrogenase XoxF, followed by oxidation of formaldehyde via the glutathione-linked oxidation pathway, subsequent oxidation of formate via formate dehydrogenases, and finally assimilation of CO2 via the Calvin-Benson-Bassham (CBB) cycle. Transcriptomics revealed upregulation of the aforementioned pathways in Bradyrhizobium sp. USDA 3456 during growth with methanol. Enzymatic assays demonstrated increased activity of the glutathione-linked oxidation pathway and formate dehydrogenases in all strains during growth with methanol compared to succinate. [13]C-labeling studies confirmed the presence of CBB intermediates and label incorporation during growth with methanol. Our findings provide multiple lines of evidence supporting the proposed XoxF-CBB pathway and, combined with genomic analyses, suggest that this metabolism is widespread among Bradyrhizobium and Sinorhizobium species.IMPORTANCENitrogen-fixing soil bacteria such as Bradyrhizobium and Sinorhizobium promote plant growth while reducing dependence on artificial, energy-intensive fertilizers. Numerous studies have attempted to increase bacterial nitrogen fixation and colonization of plant tissues by identifying the micronutrients and plant exudates that promote successful symbiotic relationships. Among the compounds encountered by rhizobacteria, lanthanides have received little attention, despite reports that plant growth is affected by the presence of lanthanides. We characterized three agriculturally relevant Bradyrhizobium and Sinorhizobium strains, demonstrated that they gain the capacity to utilize methanol when lanthanides are present, and experimentally determined the pathway by which this metabolism occurs. This study provides a foundation for understanding the lanthanide-dependent metabolism of Bradyrhizobium and Sinorhizobium, which may influence their physiology and abundance in the environment.},
}

@article {pmid41116206,
year = {2025},
author = {Hang, B and Wang, Y},
title = {Interplay between gut microbiota and intestinal lipid metabolism:mechanisms and implications.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {10},
pages = {961-971},
doi = {10.1631/jzus.B2500102},
pmid = {41116206},
issn = {1862-1783},
support = {32271213 and 32471189//the National Natural nce Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Lipid Metabolism ; Animals ; Intestinal Mucosa/metabolism ; Homeostasis ; Dysbiosis ; Obesity/metabolism ; *Intestines/microbiology ; Non-alcoholic Fatty Liver Disease/metabolism ; Metabolic Diseases/metabolism ; },
abstract = {The gut microbiota is an indispensable symbiotic entity within the human holobiont, serving as a critical regulator of host lipid metabolism homeostasis. Therefore, it has emerged as a central subject of research in the pathophysiology of metabolic disorders. This microbial consortium orchestrates key aspects of host lipid dynamics-including absorption, metabolism, and storage-through multifaceted mechanisms such as the enzymatic processing of dietary polysaccharides, the facilitation of long-chain fatty acid uptake by intestinal epithelial cells (IECs), and the bidirectional modulation of adipose tissue functionality. Mounting evidence underscores that gut microbiota-derived metabolites not only directly mediate canonical lipid metabolic pathways but also interface with host immune pathways, epigenetic machinery, and circadian regulatory systems, thereby establishing an intricate crosstalk that coordinates systemic metabolic outputs. Perturbations in microbial composition (dysbiosis) drive pathological disruptions to lipid homeostasis, serving as a pathogenic driver for conditions such as obesity, hyperlipidemia, and non-alcoholic fatty liver disease (NAFLD). This review systematically examines the emerging mechanistic insights into the gut microbiota-mediated regulation of intestinal lipid metabolism, while it elucidates its translational implications for understanding metabolic disease pathogenesis and developing targeted therapies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Lipid Metabolism
Animals
Intestinal Mucosa/metabolism
Homeostasis
Dysbiosis
Obesity/metabolism
*Intestines/microbiology
Non-alcoholic Fatty Liver Disease/metabolism
Metabolic Diseases/metabolism

@article {pmid41114582,
year = {2025},
author = {Zhang, Z and Wang, Z and Teng, P and Yu, T and Zhang, Y},
title = {Oxygen-tolerant nitrogen fixation in a marine alga-colonizing Planctomycetota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131625},
doi = {10.1128/aem.01316-25},
pmid = {41114582},
issn = {1098-5336},
abstract = {UNLABELLED: The microbiomes colonizing macroalgal surfaces orchestrate nutrient fluxes and symbiotic interactions within the algal environment. Among these communities, Planctomycetota are often dominant taxa. Although nitrogenase (nif) gene clusters have been identified in Planctomycetota isolates and metagenome-assembled genomes, functional validation of nitrogen fixation in pure culture has remained elusive. Moreover, the mechanisms enabling these bacteria to overcome oxygen sensitivity and fix nitrogen in algal-associated oxic niches remain unexplored. Here, we isolated Crateriforma sp. HD03, a Planctomycetota strain from the surface of Saccharina japonica (kelp), and provided the first experimental evidence of nitrogen-fixing activity in pure-cultured Planctomycetota. Strain HD03 harbors a complete nifHDKBEN gene cluster and exhibits a remarkable nitrogen fixation rate of 14.2 ± 1.5 nmol C2H4/(10[7] cells)/h under aerobic conditions. Genomic and physiological analysis reveals a suite of adaptations that likely mitigate oxygen stress, including genes associated with biofilm formation, hopanoid lipid synthesis, FeSII protein, hydrogenase, and bacterial microcompartments. Notably, while strain HD03 demonstrates oxygen-tolerant nitrogen fixation in pure culture, co-culture experiments with kelp under a photoperiod revealed that nifH (nitrogenase reductase gene) expression peaks during the low-oxygen dark phase, indicating that HD03 utilizes diurnal rhythms to temporally separate nitrogen fixation from photosynthetic oxygen production. A genomic survey of 142 Planctomycetota strains from NCBI GenBank database and HD03 identified two distinct clades harboring complete nifHDK gene clusters, suggesting a nitrogen-fixing potential across the phylum. By bridging the gap between genomic potential and functional validation, this study establishes Planctomycetota as important but underappreciated contributors to marine nitrogen input.

IMPORTANCE: Planctomycetota are abundant colonizers of macroalgal surfaces, yet their role in nitrogen fixation has remained unresolved despite genomic evidence of nitrogenase (nif) genes. Until now, no functional validation of nitrogen fixation in pure-cultured Planctomycetota has been reported. Here, we isolated Crateriforma sp. HD03 from kelp and for the first time demonstrated its ability to fix nitrogen in pure culture, confirming this key metabolic potential in marine Planctomycetota. Strain HD03 overcomes oxygen stress through a combination of biofilm formation and diurnal regulation of nifH expression, allowing nitrogen fixation under aerobic conditions to cope with the algal environment's oxic nature. Furthermore, genomic surveys revealed nitrogen fixation gene clusters across multiple Planctomycetota clades, suggesting widespread nitrogen-fixing capability in this phylum. Collectively, these findings identify Planctomycetota as important nitrogen providers in the ocean.},
}

@article {pmid41114576,
year = {2025},
author = {Ruiz-González, C and Mena, C and Cornejo-Castillo, FM and Romano-Gude, D and Arandia-Gorostidi, N and Gasol, JM},
title = {Diverse Patescibacteria assemblages and prevalence of ultra-small free-living Parcubacteria along a subterranean estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0112525},
doi = {10.1128/msystems.01125-25},
pmid = {41114576},
issn = {2379-5077},
abstract = {UNLABELLED: Patescibacteria are a group of novel, mostly uncultivated bacteria characterized by ultra-small cell sizes and streamlined genomes. They are ubiquitous in diverse ecosystems, often prevailing in subsurface environments, yet basic aspects such as variability in cell size, abundance, and niche preferences of different taxa within Patescibacteria remain unknown, particularly along salinity gradients. Combining flow cytometry, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), and 16S rRNA gene sequencing, we characterized Patescibacteria assemblages along a Mediterranean subterranean estuary resulting from the mixing of fresh groundwater with seawater. Patescibacteria occupied the entire subterranean salinity gradient through the replacement of taxa prevailing in fresh (Magasanikbacteria, Jorgensenbacteria UBA9983), brackish (Portnoybacteria, Yanosfkybacteria, and Peribacteria), and saline groundwater (Nomurabacteria, unidentified Gracilibacteria). Most of the detected ASVs showed less than 95% similarity to their closest match, pointing to high novelty within coastal groundwater Patescibacteria. Flow cytometry unveiled a clear population of ultra-small prokaryotes that increased in abundance from fresh to saline groundwater, and which coincided with the presence of free-living minute coccoid cells identified as Parcubacteria by CARD-FISH. Some symbiotic-like associations with prokaryotes and eukaryotes were also observed, at least within Parcubacteria. These results provide one of the rare visual observations of Patescibacteria, and the substantial diversity of yet-unidentified taxa suggests an overlooked importance of this group in coastal groundwater.

IMPORTANCE: Patescibacteria are an enigmatic group of bacteria of ultra-small sizes and reduced genomes, commonly found in subsurface environments but largely unexplored in terms of their ecological roles. Despite being present in both freshwater and marine systems, no study has explored how they distribute along salinity gradients. This study provides new insights into their distribution, diversity, and niche partitioning along a Mediterranean subterranean estuary characterized by a strong salinity gradient. We show that Patescibacteria taxa seem to adapt to varying groundwater salinity conditions, displaying a remarkable capacity to occupy fresh, brackish, and saline niches through changes in composition. The identification of ultra-small coccoid cells and symbiotic-like associations highlights a diversity of lifestyles within these groups and provides one of the scarce visual proofs of Patescibacteria. With most detected taxa being highly novel, these findings point to an overlooked importance of Patescibacteria in coastal aquifers, biogeochemically active sites ubiquitous along most coastlines.},
}

@article {pmid41114144,
year = {2025},
author = {Shoaib, M and Li, G and Liu, X and Arshad, M and Zhang, H and Asif, M and Brestic, M and Skalicky, M and Wu, J and Zhang, S and Hu, F and Li, H},
title = {Nanoplastic alters soybean microbiome across rhizocompartments level and symbiosis via flavonoid-mediated pathways.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1676933},
pmid = {41114144},
issn = {1664-462X},
abstract = {Plastic pollution, particularly its breakdown into nanoplastics (NPs), poses a significant threat to ecosystem services, with notable effects on soil-plant-microbe interactions in agricultural systems. However, there is limited understanding of how NPs influence the soil microbiome and plant symbiotic functions. In this study, we applied polypropylene (PP) and polyethylene (PE) NPs, measuring 20 to 50 nm, to soybean growing conditions. We evaluated soil physicochemical properties, nodule counts, nitrogenase activity, and bacterial community composition in nodule, rhizosphere, and bulk soil under different concentrations of these NPs (200, 500, and 1000 mg/kg of soil w/w). Our results revealed that the impact of NPs on soil physicochemical properties was type-dependent, with PE-NPs exerting a more pronounced effect on soil enzyme activities than PP-NPs. Both NPs treatments accelerated nodulation and increased nitrogenase activity, with lower doses inducing more significant effects. Furthermore, PE and PP-NPs enriched bacterial species such as Ensifer and Arthrobacter, which positively interact with diazotrophs such as Bradyrhizobium, supporting symbiosis and biological nitrogen fixation. NPs treatments also significantly affected the bacteriome assembly process in the bulk soil, rhizosphere, and nodule, with an increased source ratio from the rhizosphere to the nodule and homogenous selection in the nodule bacteriome, likely benefiting bacteria involved in nodulation. Exposure to 500 mg/kg of both NPs caused alterations in the metabolic exudation profile of the plant rhizosphere, particularly influencing the biosynthesis pathways of flavonoids and isoflavonoids. Metabolites such as genistein and naringenin emerged as key mediators of plant-microbe interactions, further enhancing plant symbiotic processes under NPs exposure. This study demonstrates that NPs influence plants' symbiotic potential both directly, by altering the composition of the soil bacteriome, and indirectly, by affecting exudation potential. It provides strong evidence that NPs, especially those smaller than a micrometer, can have long-term effects on the stability and functionality of agricultural ecosystems.},
}

@article {pmid41113655,
year = {2025},
author = {Mote, S and De, K and Nanajkar, M and Gupta, V},
title = {Unraveling the bacterial composition of a coral and bioeroding sponge competing in a marginal coral environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550446},
pmid = {41113655},
issn = {1664-302X},
abstract = {The newly described bioeroding sponge Cliona thomasi, part of the Cliona viridis complex, is contributing to coral decline in the central eastern Arabian Sea, the West Coast of India. While its morphological and allelopathic mechanisms in coral invasion are well investigated, the role of its microbial communities in spatial competition is underexplored. This study focuses on the coral Turbinaria mesenterina and sponge C. thomasi, both known for their distinct symbiotic associations with Symbiodiniaceae. A 16S rRNA V3-V4 amplicon next-generation sequencing approach, followed by processing through the DADA2 algorithm, was used to analyze the bacterial composition. The results showed higher bacterial richness and diversity in coral samples, identifying 30 distinct phyla, compared to 14 in sponge samples. The coral samples were dominated by Proteobacteria, Actinobacteria, Firmicutes, Cyanobacteria, Planctomycetes, Chloroflexi, and Patescibacteria, while Proteobacteria, Cyanobacteria, Planctomycetes, and Actinobacteria were dominant in the sponge. Enrichment analysis revealed higher dominance of Acidobacteria, Actinobacteria, Chloroflexi, Dadabacteria, Firmicutes, Fusobacteriota, and Patescibacteria in the coral samples, while the sponge samples showed enrichment for Cyanobacteria, Planctomycetes, and Bdellovibrionota. Beta-diversity analysis (PERMANOVA and nMDS) showed significant differences, with an average dissimilarity of 81.44% between sponge and coral samples (SIMPER). These differences highlight variations in microbial profiles between sponges and corals, competing in the same vulnerable environment. Exploring the microbiome aspect, therefore, may elucidate physiological and ecological functions of the holobiont while also representing a health status biomarker for corals, supporting their conservation.},
}

@article {pmid41110358,
year = {2025},
author = {Zhang, M and Huang, Q and Liu, H and Fu, H and Cao, L and Wei, H and Yan, R and Wang, W and Zhang, K and Zhang, Q},
title = {Sulfurized nano zero-valent iron loaded graphene oxide enhances the anaerobic fermentation treatment of swine manure: Insights from microbial community analysis and DFT calculations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127622},
doi = {10.1016/j.jenvman.2025.127622},
pmid = {41110358},
issn = {1095-8630},
abstract = {To enhance anaerobic treatment of livestock and poultry waste, the integration of nano-zero-valent iron and graphene oxide has been explored, given their individual limitations. This study introduced a vulcanization-modified nZVI supported on GO (S-nZVI@GO), aiming to augment reactivity in pig manure treatment. The removal rate of COD (74.00 %) and methane production (104.92 mL/g VS) were improved significantly by employing S-nZVI@GO with S/Fe = 0.04:1 and GO/S-nZVI = 0.08:1. Due to the presence of Firmicutes and Bacteroidetes bacteria and S-nZVI@GO with the change of pH, the yield of acetic acid was increased, which optimized the anaerobic fermentation with pig manure as substrate. Microbial community characteristics indicate that a high GO/S-nZVI mass ratio favors an increase in methanogen abundance, with Methanosarcina in Halobacterota exhibiting the highest abundance increase of 18.10 %, stable microbial symbiotic metabolism promote the anaerobic fermentation of pig manure. In conjunction with density functional theory computations, this study has, for the first time, elucidated the two principal routes by which S-nZVI@GO contributes to methane generation within anaerobic fermentation systems: the first entails the conversion of monosaccharides into glyceraldehyde, which is subsequently isomerized into lactic acid, ultimately yielding acetic acid and CO2; the second involves the transformation of monosaccharides into glycolaldehyde, with the intermediate product directly producing acetic acid. This research provides a theoretical foundation for the modification of iron-based materials and their composite applications with carbon-based matrices, offering significant guidance for optimizing the anaerobic fermentation process in the utilization of livestock and poultry manure resources.},
}

@article {pmid41110306,
year = {2025},
author = {Bi, K and Yang, W and Lin, Q and Lu, K and Zhu, J},
title = {Quantifying the relative contributions of different sources to the gut microbiota of Bellamya aeruginosa under cyanobacterial bloom stress.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119223},
doi = {10.1016/j.ecoenv.2025.119223},
pmid = {41110306},
issn = {1090-2414},
abstract = {Freshwater snails play a vital role in aquatic ecosystems. However, their primary activity zones often overlap with the accumulation zones of cyanobacterial scum during bloom events, resulting in direct exposure to cyanobacteria and their toxins. Cyanobacterial bloom exposure often alters the symbiotic microbiota of gastropods and consequently affects the survival of host snails. This study focused on Bellamya aeruginosa as the research subject, investigating the effects of cyanobacterial blooms on the ultrastructure, microcystin accumulation and enzyme activity in hepatopancreas. Furthermore, 16S rRNA gene sequencing was employed to characterize the composition and potential sources of gut and fecal under cyanobacterial bloom stress. Our results demonstrate that cyanobacterial blooms substantially reshaped the gut microbiota of B. aeruginosa, reducing bacterial richness and diversity in the gut, feces, and surrounding water. Community composition of environmental and host-associated microbiota shifted markedly between non-bloom and bloom periods; meanwhile, Microcystis became more prevalent in fecal microbiota than in the gut microbiota. SourceTracker analysis indicates that bacteria from the sediment are the main source of gut microbiota during non-bloom period, whereas during bloom period, bacteria from the water became the major contributors, and they were also acting as the primary source of cyanobacteria in feces. These characteristics were further supported by structural equation modeling and random forest analysis. By elucidating the shifts in host-associated and environmental microbiomes under cyanobacterial bloom stress, this study reveals alterations in the microbiota sources of B. aeruginosa and provides a theoretical framework for ecological risk assessment and pollution management in eutrophic aquatic ecosystems.},
}

@article {pmid41110288,
year = {2025},
author = {Wang, H and He, Y and Liu, M and Shen, Z and Zhang, W and Zhang, Z and Pu, X},
title = {Mycelial pathway carbon input enhances nitrogen utilization in cotton more than the root pathway in symbiotic relationships.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt C},
pages = {110620},
doi = {10.1016/j.plaphy.2025.110620},
pmid = {41110288},
issn = {1873-2690},
abstract = {Plant roots and arbuscular mycorrhizal fungi (AMF) significantly impact soil carbon (C) and nitrogen (N) processes. However, it remains unclear whether there are differences in the priming effects of new C input from roots and extraradical mycelia under different N application rates in agricultural fields, and how these differences affect crop N uptake. Therefore, this study used upland cotton (Xinluzao No. 84) as the experimental material and employed a two-chamber partitioned growth system (length × width × height: 13 × 10 × 13 cm) to investigate the effects of different N application rates (1.5, 1 and 0 g per device) on soil microbial activity, the priming effects induced by C inputs from roots and mycelia, and the N uptake by roots and mycelia. This study found that, compared to no N fertilizer, root and mycelial C inputs under reduced N condition increased soil organic carbon (SOC) by 17.2 % and 73.7 %, respectively. Furthermore, the content of mycelial C input showed a significant negative correlation with the soil original C content (P < 0.05), whereas root C input exhibited a positive correlation (P < 0.01). Additionally, the study revealed a significant positive linear relationship between the mycelia to cotton N contribution and SOC content (P < 0.05), as well as significantly higher activities of soil extracellular enzymes (e.g., PPO and NAG) via the mycelial pathway compared to the root pathway under the same N rates. These results demonstrate that new C input from mycelia under reduced N condition induced a positive priming effect, thereby enhancing the decomposition and utilization of N-containing organic matter in agricultural soil. Concurrently, N reduction increased the uptake of soil NO3[-]-N by the mycelia. Ultimately, the timely release of stored N by the mycelia, coupled with its functional shift from parasitism to symbiosis, significantly enhanced N delivery to the host plant. In contrast, as a component of soil new C input, root C input induced a negative priming effect, which contributed to soil C accumulation and helped maintain the balance of the soil C pool. These findings provide important insights into the mechanisms by which plant-AMF symbiosis regulates soil C- N process under different N conditions, and hold significant implications for improving N use efficiency and promoting sustainable agricultural development.},
}

@article {pmid41109795,
year = {2025},
author = {Ghataora, JS and Ellis, T},
title = {Rewiring holobiont systems with synthetic biology.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.09.017},
pmid = {41109795},
issn = {1879-3096},
abstract = {Holobionts are complex communities comprising a host and its diverse microbiota. Their intricate relationships are crucial for biological processes like nutrient uptake, immune function, and environmental adaptation. However, understanding these complex interactions remains challenging. We review how synthetic biology can help address these challenges. We highlight advances in bacterial biosensor design, engineering interkingdom communication, surface display, and clustered regularly interspaced short palindromic repeats (CRISPR) systems to both understand and manipulate holobiont interactions. We also highlight progress in engineering non-model microbiota members and provide rationale for a new field at the intersection of holobiont research and synthetic biology, which we term de novo holobiont design. The integration of synthetic biology with holobiont research promises to deepen our understanding of host-microbiota relationships and open new frontiers in biotechnology.},
}

@article {pmid41108161,
year = {2025},
author = {Ghantasala, S and Roy Choudhury, S},
title = {Legume Lessons: Structural and Functional Advancements in Nod Factor Receptors for Translating Root Nodule Symbiosis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf443},
pmid = {41108161},
issn = {1460-2431},
abstract = {Translating the nitrogen-fixing ability of legume-rhizobia symbiosis to other crops has long been a dream for molecular biologists. Over the past two decades, several crucial genes involved in the pathway have been identified, that prevails as an intricate network governing root nodule symbiosis (RNS). RNS signaling employs the common symbiotic signaling pathway required for Arbuscular Mycorrhizal (AM) symbiosis (plant-fungal symbiosis) that is widely known in several crop plants. Therefore, understanding the similarities and divergence between the two signaling pathways has always been a hotspot for research. The major adjuvants in the RNS pathway are the Nod Factor Receptors (NFRs - that perceive Nod Factors released by rhizobia), and a Nodule-INception protein (NIN - a transcription factor that activates cortical cell division), which direct the pathway from AMS towards RNS. Therefore, understanding the structure and the signaling mechanism(s) of NFRs and NIN is crucial for the success of translational approaches. In this article, we will be highlighting the most recent discoveries pertaining to the functionality of NFRs, which have taken us a few steps closer towards receptor engineering into non-nodulating plants.},
}

@article {pmid41107452,
year = {2025},
author = {Zhou, Y and Gutiérrez-Preciado, A and Liu, Y and Moreira, D and Yakimov, MM and López-García, P and Krupovic, M},
title = {Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41107452},
issn = {2058-5276},
support = {ANR-23-CE13-022//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-21-CE11-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0016//Agence Nationale de la Recherche (French National Research Agency)/ ; GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; ERC-2023-AdG 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Nested symbioses, including hyperparasitism in which parasites exploit other parasites within a host, are common in nature. However, such nested interactions remain poorly studied in archaea. Here we characterize this phenomenon in ultra-small archaea of the candidate phylum Nanohaloarchaeota, members of the DPANN superphylum (named after its first representative phyla: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) that form obligate interactions with halophilic archaea of the class Halobacteria. We reconstructed the viromes from geothermally influenced salt lakes in the Danakil Depression, Ethiopia, and find that nanohaloarchaea and haloarchaea are both associated with head-tailed, tailless icosahedral, pleomorphic and spindle-shaped viruses, representing 16 different families. These viruses exhibit convergent adaptation to hypersaline environments, encode diverse auxiliary metabolic genes and exchange genes horizontally with each other. We further characterize plasmid-derived satellites that independently evolved to parasitize spindle-shaped viruses of haloarchaea and nanohaloarchaea, revealing another layer of nested symbiosis. Collectively, our findings highlight the complexity of virus-host and virus-virus interactions in hypersaline environments.},
}

@article {pmid41106607,
year = {2025},
author = {Hu, T and Pu, Y and Qin, Y},
title = {Silicate intervention in Navicula-bacteria symbiosis system: nitrogen removal performance and microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133516},
doi = {10.1016/j.biortech.2025.133516},
pmid = {41106607},
issn = {1873-2976},
abstract = {To address the long-term instability of the Navicula-bacteria symbiosis system, this study achieved stable autotrophic nitrogen removal by adding silicates and regulating light/dark cycles. The nitrite accumulation rate reached 92.05 % during the enrichment of Navicula sp. (a diatom genus), which became the dominant algae with the supplementation of silicate and enhanced extracellular polymeric substances (EPS) production. The increased EPS promoted the formation of dense biofilms, facilitating the growth of anaerobic microorganisms. When the ratio of light/dark was adjusted to 8 h:16 h, the system achieved the highest total nitrogen removal rate of 82.69 %. Nitrosomonas (1.26 %) was the dominant bacteria in ammonia-oxidizing bacteria. Denitratisoma (3.75 %) was the dominant bacteria in denitrifying bacteria. Anaerobic ammonia-oxidizing bacteria were naturally enriched without artificial inoculation. The relative abundance of Candidatus Brocadia reached 7.99 %. This study demonstrates an autotrophic pathway for sustainable wastewater treatment.},
}

@article {pmid41106584,
year = {2025},
author = {Knight, HJ and McKinley, KO and Tsaousis, AD and Dodd, JA and Rückert, S},
title = {The effect of gregarine (Apicomplexa) colonisation on the functional response of the amphipod host.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.10.002},
pmid = {41106584},
issn = {1879-0135},
abstract = {Gregarines are a notably understudied but widespread group of protists that colonise aquatic and terrestrial invertebrates. This limited understanding of gregarines and their interactions with their hosts results partly from the absence of established culturing techniques and our understanding therefore has heavily relied on field collections. This study utilised for the first time cultured Gammarus pulex populations and comparative functional response models to explore the effects of gregarine colonisation on the host's consumption of Chironomid prey. This study shows that both positive and negative G. pulex displayed a Type II functional response. There were no statistical differences in the functional response parameters between the two groups. These results suggest that, under the study conditions, gregarines may function as commensal symbionts within their G. pulex host. This is consistent with growing evidence for gregarines acting across a range of symbiotic roles within their hosts. These findings provide insight into the role of gregarines in G. pulex, an invertebrate species frequently used for field- and lab-based experiments, contributing to the evidence of the complex and varied gregarine host-symbiont interactions.},
}

@article {pmid41105922,
year = {2025},
author = {Melicher, F and Dobeš, P and Komárek, J and Faltinek, L and Korsák, M and Sýkorová, P and Houser, J and Wimmerová, M},
title = {Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70293},
pmid = {41105922},
issn = {1742-4658},
support = {730872//CALIPSOplus/ ; 21-29622S//Grantová Agentura České Republiky/ ; LM2023042//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; },
abstract = {Photorhabdus bacteria live in mutualistic relationships with Heterorhabditis nematodes, and together, they act as effective insect pathogens. These bacteria produce a diverse array of lectins, sugar-binding proteins that are believed to play crucial roles in the complex tripartite interaction among Photorhabdus, nematodes, and their insect hosts. One such lectin, Photorhabdus laumondii tumor necrosis factor (TNF)-like lectin (PLTL), identified in Photorhabdus laumondii subsp. laumondii TTO1, exhibits notable sequence similarity to the N-terminal domain of the BC2L-C lectin (BC2L-CN), a TNF-like lectin recognized for its specificity toward fucosylated glycans associated with human embryonic stem cells and certain cancers. Through glycan array analysis and surface plasmon resonance, we identified PLTL's binding preference for branched histo-blood group oligosaccharides. The crystallographic structure of PLTL in complex with the BLe[b] pentasaccharide reveals a network of direct and water-mediated hydrogen bonds simultaneously stabilizing the Fucα1-2 and Galα1-3 moieties, which define its narrow glycan specificity. A combination of mass spectrometry, protein crystallography, and analytical ultracentrifugation showed a unique hexameric PLTL architecture stabilized by intermolecular disulfide bridges. Our data suggest that PLTL may contribute to the mutualistic relationship between Photorhabdus and its nematode symbiont, Heterorhabditis bacteriophora, rather than playing a role in the interaction with the insect host. This study provides a structural and functional characterization of PLTL, a newly identified member of the TNF-like lectin family. Comparative analysis with BC2L-CN highlights both conserved and distinct structural features, suggesting potential applications in glycan recognition-based diagnostics or biotechnological tools beyond its biological role. Our findings underscore its complex glycan specificity and offer insights into its potential role in Photorhabdus-nematode symbiosis.},
}

@article {pmid41105806,
year = {2025},
author = {Moloney, A and Stuart, L},
title = {Cultural Safety and clinical safety: A symbiotic relationship for improving Aboriginal and Torres Strait Islander Peoples and Communities' health outcomes.},
journal = {Contemporary nurse},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/10376178.2025.2573155},
pmid = {41105806},
issn = {1839-3535},
abstract = {DISCUSSION: While the link between Cultural Safety and patient outcomes is clear, consistent application in practice is lacking. Cultural Safety is equally vital as clinical safety in ensuring quality care, particularly for Indigenous Australians affected by culturally unsafe practices.

RECOMMENDATIONS: In healthcare delivery Indigenous Australians health and the 'Closing the Gap' agenda is everybody's business, it is not the responsibility of the patient, their family or their Community. The authors propose a reconceptualisation of the way health and wellbeing is perceived by health professionals, in which providing culturally safe care is symbiotic with providing clinically safe care. As an integrated foundation for quality and safety in health care, this strategy brings together the social determinants of culturally safe care with competent, evidence-based, equitable and non-bias care for all, and could help advance the Closing the Gap agenda.},
}

@article {pmid41105737,
year = {2025},
author = {Li, X and An, JL and Yang, WQ and Liu, TX and Zhang, SZ},
title = {Regulation of lipid metabolism in Spodoptera frugiperda by the symbiotic bracovirus of the gregarious parasitoid Cotesia ruficrus.},
journal = {PLoS pathogens},
volume = {21},
number = {10},
pages = {e1013605},
doi = {10.1371/journal.ppat.1013605},
pmid = {41105737},
issn = {1553-7374},
abstract = {Parasitoids alter host energy homeostasis to create a favorable environment for their own development. However, the mechanisms underlying this process remain largely unexplored, especially for gregarious parasitoids. Cotesia ruficrus, a gregarious endoparasitoid native to China, targets the invasive pest Spodoptera frugiperda (fall armyworm, FAW) and has been shown to effectively control FAW populations. This study investigates the role of the polydnavirus (PDV) produced by C. ruficrus in regulating lipid metabolism of FAW larvae. The results demonstrated that, following PDV injection for 5 days, both triglyceride concentrations and lipid droplet diameters in the fat bodies of FAW larvae significantly increased. RNA interference (RNAi) targeting the PDV gene CrBV3-31 led to a reduction in triglyceride concentrations and lipid droplet size, along with an upregulation of the LSD1 gene. Furthermore, silencing CrBV3-31 decreased triglyceride levels in C. ruficrus pupae and lowered its eclosion rate. These findings suggest that the PDV gene CrBV3-31 plays a crucial role in enhancing lipid accumulation in FAW larvae, thereby supporting the survival of C. ruficrus offspring. This study uncovers a novel mechanism by which gregarious endoparasitoids exploit symbiotic bracovirus genes to regulate host energy metabolism, increasing lipid levels to meet the developmental needs of their multiple offspring.},
}

@article {pmid41105100,
year = {2025},
author = {Arellano, AA and Prack, JL and Coon, KL},
title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf233},
pmid = {41105100},
issn = {1751-7370},
abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.},
}

@article {pmid41104963,
year = {2025},
author = {Zhang, H and Weinberger, N and Powell, JR},
title = {Functional Diversity of Arbuscular Mycorrhizal Fungi Drives Divergent Plant Resource Allocation Strategies Under Nitrogen Limitation.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf459},
pmid = {41104963},
issn = {1460-2431},
abstract = {Arbuscular mycorrhizal (AM) fungi shape plant nutrient acquisition, yet their functional roles under nitrogen (N) limitation remain unclear. Using Plantago lanceolata inoculated with five AM fungi strains under N-limited conditions, we demonstrate that fungal identity critically regulates symbiotic outcomes. Despite interspecific variation in extraradical mycelium production and hyphal traits (carbon/nitrogen/phosphorus concentrations [C/N/P], diameter), AM fungi universally failed to enhance plant biomass. We identified three plant-AM fungal phenotypic strategies under N-limitation: (1) high mycelial investment with carbon drain (Rhizophagus irregularis WFVAM23, Funneliformis mosseae WFVAM45), where sustained fungal growth reduced shoot biomass; (2) early mycelial growth with root trait modulation (R. irregularis DAOM10, Scutellospora calospora WFVAM35), showing rapid initial mycelial growth that plateaus, exerting neutral effects on plant biomass. Meanwhile, S. calospora WFVAM35 reduced root diameter while R. irregularis DAOM10 increased RTD; and (3) low mycelial production with minimal host impact (Gigaspora margarita WFVAM21), with minimal mycelial biomass across all growth stages. AM fungi functional diversity reshapes plant resource allocation across a mutualism-parasitism spectrum under N limitation, mediated by fungal mycelium traits and root architectural reconfiguration. N availability and fungal identity emerge as pivotal determinants of mycorrhizal phenotypic plasticity, emphasizing the critical role of trait-based frameworks to predict plant-fungal adaptation dynamics in nutrient-limited ecosystems.},
}

@article {pmid41103917,
year = {2025},
author = {Iorizzo, M and Ganassi, S and Testa, B and Di Donato, LM and Albanese, G and Succi, M and Coppola, F and Cozzolino, R and Matarazzo, C and Di Criscio, D and Tedino, C and De Cristofaro, A},
title = {Ascosphaera apis as a target for the antifungal activity of symbiotic Bifidobacteria in honey bees.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1669013},
pmid = {41103917},
issn = {2673-8600},
abstract = {INTRODUCTION: The genus Bifidobacterium is a key component of the honey bee gut microbiota, playing a fundamental role in maintaining host health and colony well-being. Alongside other core genera such as Bombilactobacillus, Gilliamella, Lactobacillus, and Snodgrassella, Bifidobacterium contributes to essential functions including nutrient digestion, immune modulation, and protection against pathogens. Among threats to honey bee health, Chalkbrood disease, caused by fungus Ascosphaera apis, remains a major concern due to detrimental effects on colony strength and honey yield.

MATERIALS AND METHODS: We characterized enzymatic activity and carbohydrate assimilation of nine Bifidobacterium strains isolated from the honey bee intestinal tract. In parallel, we assessed antifungal potential against A. apis strains, focusing on volatile organic compounds (VOCs).

RESULTS AND DISCUSSION: Notably, Bifidobacterium asteroides 3CP-2B exhibited enzymatic capabilities supporting digestive functions and metabolism of sugars potentially harmful to honey bees. This strain showed marked antifungal activity against A. apis, mediated by volatile and non-volatile bioactive metabolites. Among VOCs identified, propanoic acid, ethanol, acetic acid, ethyl propionate, and 1-propanol were the most prominent compounds associated with the antifungal effect.},
}

@article {pmid41102371,
year = {2025},
author = {Liu, S and Gao, Y and Wu, S},
title = {Diversity and Antimicrobial Activity of Potential Endophytic Fungi Isolated from the Medicinal Plant Gmelina arborea.},
journal = {Current microbiology},
volume = {82},
number = {12},
pages = {561},
pmid = {41102371},
issn = {1432-0991},
support = {grant No. 32260110//National Natural Science Foundation of China/ ; },
mesh = {*Endophytes/classification/isolation & purification/genetics/physiology ; *Fungi/classification/isolation & purification/genetics/physiology ; *Plants, Medicinal/microbiology ; Phylogeny ; *Verbenaceae/microbiology ; *Anti-Infective Agents/pharmacology/metabolism ; *Biodiversity ; Plant Roots/microbiology ; Microbial Sensitivity Tests ; Bacteria/drug effects ; Plant Leaves/microbiology ; },
abstract = {Gmelina arborea, a medicinal plant belonging to the Verbenaceae family, is extensively utilized in Ayurveda, the traditional Indian medical system. Endophytic fungi, which engage in mutualistic symbiosis with host plants, are recognized as significant microbial resources due to their ability to produce a diverse array of bioactive compounds. In this study, 131 potential endophytic fungal isolates were obtained from the roots, stems, leaves, and flowers of G. arborea. Phylogenetic analysis classified these fungi into 3 phyla, 6 classes, 13 orders, 23 families, and 27 genera. Diversity analysis indicated significant variations in isolation frequency among different tissues, with the highest frequency observed in roots, followed by flowers, leaves, and stems. The dominant genera identified were Diaporthe (17.6%), Fusarium (12.2%), and Mucor (12.2%). Antimicrobial screening against seven pathogenic microorganisms demonstrated that 23 potential endophytic strains (17.6%) exhibited significant inhibitory activity. These findings establish a foundation for further investigation into the antagonistic capabilities of potential endophytic fungi from G. arborea against pathogens and provide valuable insights into their diversity.},
}

*Endophytes/classification/isolation & purification/genetics/physiology
*Fungi/classification/isolation & purification/genetics/physiology
*Plants, Medicinal/microbiology
Phylogeny
*Verbenaceae/microbiology
*Anti-Infective Agents/pharmacology/metabolism
*Biodiversity
Plant Roots/microbiology
Microbial Sensitivity Tests
Bacteria/drug effects
Plant Leaves/microbiology

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

@article {pmid41100614,
year = {2025},
author = {Nishino, T and Moriyama, M and Mukai, H and Tanahashi, M and Hosokawa, T and Chang, HY and Tachikawa, S and Nikoh, N and Koga, R and Kuo, CH and Fukatsu, T},
title = {Defensive fungal symbiosis on insect hindlegs.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6770},
pages = {279-283},
doi = {10.1126/science.adp6699},
pmid = {41100614},
issn = {1095-9203},
mesh = {Animals ; *Symbiosis ; Female ; Hyphae/growth & development/physiology ; Wasps/physiology ; Oviposition ; *Heteroptera/microbiology/anatomy & histology ; *Hypocreales/physiology ; Ovum/microbiology ; },
abstract = {Dinidorid stinkbugs were reported to possess a conspicuous tympanal organ on female hindlegs. In this study, we show that this organ is specialized to retain microbial symbionts rather than to perceive sound. The organ's surface is not membranous but consists of porous cuticle in which each pore connects to glandular secretory cells. In reproductive females, the hindleg organ is covered with fungal hyphae that grow from the pores. Upon oviposition, the females transfer the fungi from the organ to the eggs, where the hyphae physically protect the eggs against wasp parasitism. The fungi comprise a diversity of mostly low-pathogenicity Cordycipitaceae.},
}

Animals
*Symbiosis
Female
Hyphae/growth & development/physiology
Wasps/physiology
Oviposition
*Heteroptera/microbiology/anatomy & histology
*Hypocreales/physiology
Ovum/microbiology

@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}

@article {pmid41098857,
year = {2025},
author = {Schurr, A},
title = {Glioma neuron symbiosis: a hypothesis.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1646148},
pmid = {41098857},
issn = {1662-4548},
abstract = {Glioma cells, just like all cancerous cells, consume substantial amounts of glucose for their energy needs, using glycolysis, an inefficient metabolic pathway (Warburg effect) to produce only two moles of adenosine triphosphate and two moles of lactate for each mole of glucose consumed. By contrast, neurons consume glucose via glycolysis and utilize its end-product lactate as the substrate of the mitochondrial tricarboxylic acid cycle and its coupled oxidative phosphorylation, a process eighteen times more efficient at adenosine triphosphate than glycolysis alone. It hypothesizes here that glioma-produced lactate is the preferred oxidative energy substrate of their surrounding neurons. Consequently, by using lactate, neurons bypass glycolysis, sparing their glucose and making it readily available for the glucose-craving cancer cells. Moreover, glioma cells' ability to secrete glutamate, which excites glutamatergic neurons, could drive the latter to consume even more lactate, sparing more glucose. Such symbiotic exchange, especially at the initial stages of malignancy, assures the budding cancer cells an ample glucose supply ahead of the development of additional vasculature. While this hypothesis focuses on gliomas, it may also apply to other cancer types.},
}

@article {pmid41097855,
year = {2025},
author = {Ou, H and Xie, D and Yao, R and Shan, X},
title = {Strigolactones: Biosynthesis, transport, perception and signal transduction.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.10.008},
pmid = {41097855},
issn = {1752-9867},
abstract = {Strigolactones (SLs) are carotenoid-derived phytohormones that regulate plant development and mediate rhizosphere interactions. Synthesized from β-carotene through a multistep enzymatic pathway, SLs modulate key physiological processes, including shoot branching, leaf development, flowering, and root growth. Beyond their endogenous roles, SLs are exuded into the soil, where they serve as ecological signals. The exuded SLs facilitate symbiotic relationships with arbuscular mycorrhizal fungi (AMF) for nutrient exchange, while also are exploited by parasitic weeds to locate host plants. Although the core SL biosynthesis and signaling pathways have been elucidated, emerging research continues to uncover new layers of complexity in their regulation and function. Here, we present a comprehensive overview of SLs, summarizing and updating current knowledge and recent advances in their biosynthesis, transport, perception and signal transduction, along with their multifaceted functions. Moreover, we discuss the challenges currently faced in SL research and identify urgent questions for future investigation. Addressing these issues would further enhance our understanding of the SL pathway and promote its application in agriculture.},
}

@article {pmid41097293,
year = {2025},
author = {Besharati, M and Ciavatta, ML and Carbone, M and Cacciapuoti, N and Aversa, M and Roscetto, E and Castaldi, S and Perrone, G and Boari, A and Gialluisi, K and Catania, MR and Moosawi-Jorf, SA and Evidente, A},
title = {Extraction and Identification of the Bioactive Metabolites Produced by Curvularia inaequalis, an Endophytic Fungus Collected in Iran from Echium khuzistanicum Mozaff.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {19},
pages = {},
doi = {10.3390/molecules30193870},
pmid = {41097293},
issn = {1420-3049},
support = {Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP B83C22002930006//National Biodiversity Future Center - NBFC supported by European Commission - NextGeneration EU Project and funded by the Italian Ministry of University and Research (PNRR, Mission 4 Component 2, "Dalla ricerca all'impresa", Investimento 1.4, CN00000033)/ ; },
mesh = {*Ascomycota/chemistry/metabolism ; Iran ; *Endophytes/chemistry/metabolism ; *Echium/microbiology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification ; Plants, Medicinal/microbiology ; },
abstract = {Endophytic fungi (EF) are microorganisms that colonize the internal tissues of host plants, providing a range of benefits to them. In this symbiosis, they act as a reservoir of bioactive metabolites that are important for enhancing the host's defense mechanisms as a resistance against pathogens. These molecules usually possess antimicrobial properties that can be exploited for application in agriculture and medicine. In this context, the current work was designed to evaluate the phytotoxic and antimicrobial properties of the endophytic fungus Curvularia inaequalis, isolated for the first time from the Iranian medicinal plant Echium khuzistanicum. Culture filtrates, their organic extracts, and isolated metabolites were tested against a series of plants to assess their phytotoxicity, as well as against a wide range of plant and human pathogens to evaluate their antimicrobial activity. The main compounds characterizing the organic extract of C. inaequalis have been identified as (R)-phomalactone, catenioblin A, and (-) asperpentyn (1-3) by using spectroscopic techniques, NMR mainly, and HR-ESI-MS. In the bioactivity evaluation carried out in this study, (R)-phomalactone (1) stood out as the most promising compound, exhibiting significant non-host phytotoxic activity on tomato leaves; potent antibacterial activity against a wide range of human pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) strains; and marked antifungal activity against several economically important phytopathogens. (-)-Asperpentyn (3) also showed robust and selective antifungal activity against phytopathogens, while catenioblin A (2) exhibited only a slight phytotoxic effect and limited overall bioactivity in this study. These findings reveal that the isolated endophytic fungi hold considerable promise as an untapped source of bioactive metabolites with antibacterial, antifungal, and phytotoxic activities.},
}

*Ascomycota/chemistry/metabolism
Iran
*Endophytes/chemistry/metabolism
*Echium/microbiology
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification
Plants, Medicinal/microbiology

@article {pmid41096566,
year = {2025},
author = {Chen, J and Zhang, Y and Zhang, M and Zhang, Z and Liu, Y and Duan, X and Tao, Z and Jiang, W},
title = {Study on the Molecular Mechanism of Arbuscular Mycorrhizal Symbiosis Regulating Polysaccharide Synthesis in Dendrobium officinale.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199298},
pmid = {41096566},
issn = {1422-0067},
support = {32102485//National Natural Science Foundation of China/ ; 2025SNJF011//Three Rural Areas and Nine Directions" Science and Technology Collaboration Program of Zhejiang Province/ ; ZX2024005-1//Wenzhou Agricultural New Varieties Breeding Collaboration Group Project/ ; ZN2023005//Wenzhou Major Science and Technology Innovation Research Project/ ; },
mesh = {*Mycorrhizae/physiology/genetics ; *Dendrobium/microbiology/genetics/metabolism ; *Symbiosis/genetics ; *Polysaccharides/biosynthesis ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; Transcriptome ; Gene Expression Profiling ; Plant Roots/microbiology/metabolism ; },
abstract = {Mycorrhizal symbiosis represents a ubiquitous mutualistic relationship in nature, wherein mycorrhizal fungi enhance the host plant's ability to absorb water and nutrients from the soil. In return, the host plant supplies the fungi with essential nutrients necessary for their metabolic activities. However, research focusing on the regulatory mechanisms governing mycorrhizal symbiosis in Dendrobium officinale remains limited. This study systematically investigates the regulatory mechanisms of mycorrhizal symbiosis on transcriptional synthesis in D. officinale by establishing a mycorrhizal symbiotic system, complemented by phenotypic observation, physiological measurement, and transcriptome sequencing. The results indicate that mycorrhizal symbiosis promotes both growth and nutrient absorption in D. officinale, concurrently increasing polysaccharide content. Through transcriptome analysis, we identified 59 differentially expressed genes associated with polysaccharide metabolism, alongside key genes and transcription factors integral to the regulatory network. Notably, the glycosyltransferase gene DoUGT83A1 was found to negatively regulate the mycorrhizal symbiotic system when heterologously expressed in tomato. This study provides a fundamental theoretical basis for elucidating the molecular mechanisms underlying polysaccharide synthesis in D. officinale and offers new insights for optimizing cultivation practices to enhance medicinal quality.},
}

*Mycorrhizae/physiology/genetics
*Dendrobium/microbiology/genetics/metabolism
*Symbiosis/genetics
*Polysaccharides/biosynthesis
Gene Expression Regulation, Plant
Plant Proteins/genetics/metabolism
Transcriptome
Gene Expression Profiling
Plant Roots/microbiology/metabolism

@article {pmid41095127,
year = {2025},
author = {Kitaeva, AB and Kusakin, PG and Gorshkov, AP and Tsyganova, AV and Tsyganov, VE},
title = {Tubulin Cytoskeleton Organization in Cells of Determinate Nodules in Vigna radiata, Vigna unguiculata, and Lotus corniculatus.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/plants14192986},
pmid = {41095127},
issn = {2223-7747},
support = {24-16-00156//Russian Science Foundation/ ; },
abstract = {Tubulin cytoskeleton rearrangements play an important role in the cell differentiation of symbiotic nodules in legumes. However, the organization of the tubulin cytoskeleton has been investigated only for four legume species forming determinate nodules (with limited nodule meristem activity). In this study, microtubule organization was studied in three species (Vigna radiata, V. unguiculata, and Lotus corniculatus) with determinate nodules using confocal laser scanning microscopy and quantitative analyses. Histological organization in young nodules of V. radiata and V. unguiculata resembled the recently reported zonation in young nodules of Glycine max. In addition, bacteroids in nodules of these species were significantly enlarged compared to free-living bacteria. Organization of endoplasmic and cortical microtubules in young infected cells and uninfected cells and that of cortical microtubules in nitrogen-fixing cells demonstrated general patterns for determinate nodules, whereas endoplasmic microtubules in nitrogen-fixing cells showed species-specific patterns. Thus, the presence of both general and species-specific patterns of tubulin cytoskeleton organization was confirmed in determinate nodules.},
}

@article {pmid41095116,
year = {2025},
author = {Navarro, BB and Machado, MJ and Figueira, A},
title = {Nitrogen Use Efficiency in Agriculture: Integrating Biotechnology, Microbiology, and Novel Delivery Systems for Sustainable Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/plants14192974},
pmid = {41095116},
issn = {2223-7747},
support = {140619/2022-4//National Council for Scientific and Technological Development/ ; 140991/2022-0//National Council for Scientific and Technological Development/ ; 88887.615059/2021-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 310645/2021-2//National Council for Scientific and Technological Development/ ; },
abstract = {Nitrogen (N) is the primary macronutrient that supports global agriculture. The Haber-Bosch process revolutionized the use of synthetic N fertilizers, enabling significant increases in crop yield. However, N losses from fertilization led to negative impacts on the environment. Improving crops' N use efficiency (NUE) has been constrained by the limited understanding of N uptake and assimilation mechanisms, and the role of plant-microbe interactions. Among biological approaches, N fixation by cover crops and rhizobia symbioses represents a cornerstone strategy for improving NUE. The adoption of plant growth-promoting bacteria and arbuscular mycorrhizal fungi may enhance N acquisition by increasing root surface, modulating phytohormone levels, and facilitating nutrient transfer. Advances in plant molecular biology have identified key players and regulators of NUE (enzymes, transporters, and N-responsive transcription factors), which enhance N uptake and assimilation. Emerging biotechnological strategies include de novo domestication by genome editing of crop wild relatives to combine NUE traits and stress resilience back into domesticated cultivars. Additionally, novel fertilizers with controlled nutrient release and microbe-mediated nutrient mobilization, hold promise for synchronizing N availability with plant demand, reducing losses, and increasing NUE. Together, these strategies form a multidimensional framework to enhance NUE, mitigate environmental impacts, and facilitate the transition towards more sustainable agricultural systems.},
}

@article {pmid41094757,
year = {2025},
author = {Sharma, A and Mukherjee, S and Verma, A and Aryan, A and Chandran, D},
title = {The Pea Inner Nuclear Membrane SUN Domain Protein Modulates Plant (a)biotic Stress Responses by Regulating Nuclear Dynamics.},
journal = {Molecular plant pathology},
volume = {26},
number = {10},
pages = {e70158},
doi = {10.1111/mpp.70158},
pmid = {41094757},
issn = {1364-3703},
support = {//Regional Centre for Biotechnology/ ; //Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Plant Proteins/metabolism/genetics/chemistry ; *Pisum sativum/metabolism/genetics/microbiology ; *Stress, Physiological/genetics ; *Nuclear Envelope/metabolism ; Arabidopsis/genetics/metabolism/microbiology ; Gene Expression Regulation, Plant ; *Cell Nucleus/metabolism ; Plant Diseases/microbiology ; },
abstract = {Plant inner nuclear membrane (INM) Sad1/UNC-84 (SUN) proteins are essential for maintaining nuclear morphology, positioning and gene expression during development and environmental stress conditions. Recent studies suggest their involvement in symbiosis and pathogen defence, but their precise role in plant immunity remains unclear. Given the importance of nuclear dynamics during plant-pathogen interactions, understanding the function of SUN proteins in immune signalling is essential. Here, we identify and characterise the pea (Pisum sativum) C-terminal SUN. Using knockdown (KD) and overexpression (OE) strategies in pea and/or Arabidopsis, we demonstrate that PsSUN localises to the INM and regulates pathogen-induced nuclear positioning, nuclear morphology and defence gene expression. PsSUN-KD increased nuclear circularity and sphericity, impaired nuclear relocation to the fungal penetration site, and inhibited powdery mildew growth. PsSUN-OE deformed the nuclear envelope (NE) and enhanced defence gene expression and pathogen resistance. PsSUN-OE also increased plant abiotic stress-responsive gene expression and abscisic acid sensitivity. Furthermore, we demonstrate that interactions between PsSUN and the Arabidopsis lamin-like protein KAKU4 likely influence both their localisation at the nuclear periphery and the architecture of the NE, with the extent of these effects depending on the expression levels of the two proteins. Our results suggest that SUN and nuclear lamina coordinately regulate plant NE architecture and stress responses.},
}

*Plant Proteins/metabolism/genetics/chemistry
*Pisum sativum/metabolism/genetics/microbiology
*Stress, Physiological/genetics
*Nuclear Envelope/metabolism
Arabidopsis/genetics/metabolism/microbiology
Gene Expression Regulation, Plant
*Cell Nucleus/metabolism
Plant Diseases/microbiology

@article {pmid41094593,
year = {2025},
author = {Gervais, O and Tignat-Perrier, R and Armougom, F and Voolstra, CR and Allemand, D and Ferrier-Pagès, C},
title = {Functional stability of Spirochaetota symbionts in the precious octocoral Corallium rubrum under heat stress.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {132},
pmid = {41094593},
issn = {2524-6372},
abstract = {BACKGROUND: Octocoral gorgonians are the engineer species of the Mediterranean coralligenous assemblages, but they are threatened with collapse due to recurring marine heat waves. These extreme events disrupt their symbiotic relationship with their associated microbes, promoting pathogen proliferation and tissue-degrading diseases. While the effects of seawater warming on microbial taxonomic diversity have been extensively studied, the functional response of bacterial symbionts and opportunists to thermal stress in Mediterranean octocorals has not yet been investigated. To fill this gap, we investigated a unique and very stable symbiosis between the emblematic red coral Corallium rubrum and its Spirochaetota symbionts. Although the relative and absolute abundances of Spirochaetota are not affected by heat stress, these symbionts may lose their functions within the coral holobiont.

RESULTS: Our results infer that the Spirochaetota bacterial symbionts of C. rubrum underwent only limited functional changes in response to thermal stress, consistent with their stable abundance in coral tissue. These symbionts may play a role in enhancing the tolerance of C. rubrum to temperature fluctuations by maintaining essential amino acid and vitamin biosynthesis. However, thermal stress affected other groups of bacteria, with Gammaproteobacteria showing reduced functionality (with the exception of Vibrionales, which may contribute to the deterioration of coral health) and Alphaproteobacteria showing increased opportunistic activity. In addition, many differentially expressed genes were associated with the sulfur cycle, highlighting its key role in shaping coral-associated bacterial communities under thermal stress.

CONCLUSIONS: The stability of the bacterial symbionts of C. rubrum, especially Spirochaetota, despite thermal stress, is consistent with their constant presence in octocoral tissues. These symbionts contribute to coral resilience by maintaining essential biosynthetic processes. However, the increased activity of opportunistic and pathogenic bacteria such as Vibrio suggests that C. rubrum may be susceptible to the recurring heat waves of the summer season.},
}

@article {pmid41094138,
year = {2025},
author = {Levy, S and Grau-Bové, X and Kim, IV and Najle, SR and Księżopolska, E and Elek, A and Montes-Espuña, L and Montgomery, SA and Mass, T and Sebé-Pedrós, A},
title = {The evolution of facultative symbiosis in stony corals.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41094138},
issn = {1476-4687},
abstract = {Most stony corals are obligate symbionts that are dependent on nutrients provided by the photosynthetic activity of dinoflagellates residing within specialized cells[1]. Disruption of this symbiotic consortium leads to coral bleaching and, ultimately, mortality[2]. However, a few coral species exhibit facultative symbiosis, allowing them to survive extended periods of bleaching[3,4]. Despite this resilience, the underlying biological mechanisms remain poorly understood. Here we investigate the genomic and cellular basis of facultative symbiosis in Oculina patagonica, a thermotolerant Mediterranean coral[5,6]. We sequenced and annotated a chromosome-scale genome of O. patagonica and built cell atlases for this species and two obligate symbiotic corals. Comparative genomic analysis revealed karyotypic and syntenic conservation across all scleractinians, with species-specific gene expansions primarily driven by tandem duplications. Single-cell transcriptomic profiling of symbiotic and naturally aposymbiotic wild specimens identified an increase in phagocytic immune cells and a metabolic shift in gastrodermal gene expression from growth-related functions to quiescent, epithelial-like states. Cross-species comparison of host cells uncovered Oculina-specific metabolic and signalling adaptations indicative of an opportunistic, dual-feeding strategy that decouples survival from symbiotic state.},
}

@article {pmid41093569,
year = {2025},
author = {Ying, C and Nozawa, S and Kusakabe, S and Songwattana, P and Piromyou, P and Boonchuen, P and Tittabutr, P and Boonkerd, N and Mitsui, H and Sato, S and Teaumroong, N and Hashimoto, S},
title = {The Type III Effector NopM from Bradyrhizobium elkanii USDA61 Induces a Hypersensitive Response in Lotus japonicus Root Nodules.},
journal = {Microbes and environments},
volume = {40},
number = {4},
pages = {},
doi = {10.1264/jsme2.ME25020},
pmid = {41093569},
issn = {1347-4405},
mesh = {*Bradyrhizobium/genetics/metabolism ; *Lotus/microbiology/genetics/immunology ; Symbiosis ; *Root Nodules, Plant/microbiology/immunology/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Ubiquitin-Protein Ligases/metabolism/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {Leguminous plants establish root nodule symbiosis, which is initiated by the recognition of rhizobial nodulation factors by plant receptor kinases. However, other factors, such as Type III effector proteins, also affect host specificity. We herein investigated the role of nodulation outer protein M (NopM), a Type III effector of Bradyrhizobium elkanii USDA61, in symbiosis with Lotus japonicus MG-20 and Lotus burttii. NopM, annotated as an E3 ubiquitin ligase, triggers an early senescence-like response, inducing brown nodules that hinder effective symbiosis. NopM shares structural features with E3 ubiquitin ligases derived from both pathogenic and symbiotic bacteria, including a leucine-rich-repeat and E3 ubiquitin ligase domain. The deletion of these domains or substitution of the cysteine residue, predicted to be the active site of the ubiquitin ligase domain, suppressed the formation of brown nodules. These results suggest that NopM interacts with target proteins through its leucine-rich-repeat domain and mediates ubiquitination via its ligase domain, thereby contributing to the induction of brown nodules. A transcriptome ana-lysis further suggested that the early senescence-like response closely resembled the plant hypersensitive response, with the up-regulation of defense-related genes. Therefore, L. japonicus may recognize NopM in infected nodule cells, leading to an immune response that disrupts symbiosis. The present study provides insights into the mole-cular mechanisms by which rhizobial effectors modulate symbiotic interactions in infected nodule cells, highlighting the ability of L. japonicus to activate immune responses even in nodule cells where rhizobia have been accepted.},
}

*Bradyrhizobium/genetics/metabolism
*Lotus/microbiology/genetics/immunology
Symbiosis
*Root Nodules, Plant/microbiology/immunology/metabolism
*Bacterial Proteins/genetics/metabolism/chemistry
Ubiquitin-Protein Ligases/metabolism/genetics
Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant

@article {pmid41093294,
year = {2025},
author = {Dediu, V and Buşilă, M and Ungureanu, C and Grigore-Gurgu, L and Cotârleṭ, M and Romanitan, C and Tucureanu, V and Brincoveanu, O and Vasile, BS and Bahrim, GE},
title = {Cellulose-Silver and Cellulose-Gold Bioactive Nanocomposites Obtained Using SCOBY Purified Membranes.},
journal = {ACS applied bio materials},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsabm.5c00395},
pmid = {41093294},
issn = {2576-6422},
abstract = {The green synthesis of bioactive nanomaterials is becoming more attractive in various fields like biotechnology, pharmaceuticals, cosmeceuticals, etc. In this study, bacterial cellulose-silver and bacterial cellulose-gold bionanocomposites were obtained through an environmentally friendly and low-cost method without using additional reducing agents. In the first step, the bacterial cellulose, a byproduct from kombucha production using a symbiotic culture of bacteria and yeast (SCOBY), was purified using an alkaline solution. In the second step, the purified bacterial cellulose (SBC) was used to obtain silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) on the bacterial cellulose matrix, starting only from metal precursors in different media: water, black tea, and kombucha. Gold and silver nanoparticles were obtained on cellulose fibrils in all media, even in water, indicating the reducing role of cellulose. The morphology and structural features of the noble metal nanoparticles/bacterial cellulose nanocomposites (AgNPs/SBC and AuNPs/SBC) were investigated. Scanning electron microscopy (SEM) images show nanoparticles with an irregular shape with dimensions ranging from a few nanometers up to 70 nm, depending on the synthesis medium. TEM analysis revealed mostly quasi-spherical nanoparticles distributed along the surface of the cellulose fibers or within the interfibrillar pores. All nanoparticles are well crystallized and generally formed from more than two nanocrystallites, except AuNPs obtained in kombucha which are monocrystalline. XRD analysis shows the characteristic diffractograms of Iβ cellulose allomorphs and confirms the formation of crystalline AgNPs and AuNPs. The antioxidant capacity tests determined that the best activity was registered for the AgNPs/SBC composites obtained in kombucha and fresh black tea. The antimicrobial potential was evaluated against the Gram-negative bacteria Escherichia coli and the Gram-positive bacteria Staphylococcus aureus and Listeria monocytogenes. Cellulose-silver and cellulose-gold nanocomposites showed increased antimicrobial activity compared with raw SBC, especially in the case of kombucha medium for green synthesis. The highest antioxidant activity, determined by DPPH and ABTS assays, was obtained for AgNPs/SBC produced in kombucha and fresh black tea. Based on the results, cellulose-silver and cellulose-gold nanocomposites could be considered as bioactive materials for multiple practical applications, such as the medical field and food packaging.},
}

@article {pmid41093188,
year = {2025},
author = {Yu, L and Guo, Y and Zhang, Z and Wang, X},
title = {Genome-wide identification and functional analysis of the IQD gene family in Medicago truncatula: Implications for nodule formation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148204},
doi = {10.1016/j.ijbiomac.2025.148204},
pmid = {41093188},
issn = {1879-0003},
abstract = {Microtubule plays a key role in the process of legume-Rhizobium nodule symbiosis. The IQ67-domain (IQD) family which is a group of plant-specific microtubule associated protein, plays diverse roles in plant development and in responses to environmental stress. However, IQD family members, and which are involved in nodulation in Medicago truncatula (M. truncatula) remain unclear. In this study, 31 MtIQD genes were first identified from the M. truncatula genome and named MtIQD1-MtIQD31. Phylogenetic analysis classified these genes into five groups. All MtIQD proteins contain the highly conserved IQ67 domain, while exhibiting diverse and characteristic structural features. The promoters of the MtIQD genes contain multiple cis-acting elements associated with hormone signaling, stress responses, and developmental processes. Tissue-specific expression profiling indicated a variety of expression patterns among MtIQD gene family members. Notably, MtIQD6, MtIQD8, MtIQD17, MtIQD22, and MtIQD31 showed highly specific expression in nodules and co-localized with microtubules, suggesting a potential role in cytoskeletal dynamics. Additionally, functional analysis revealed that MtIQD22 and MtIQD31 participate in nodule formation. Together, these findings provided new insights into the evolution and functional diversification of the MtIQD gene family and establish a foundation for future research on their roles in nodule development, with potential applications in the genetic improvement of leguminous crops.},
}

@article {pmid41093027,
year = {2025},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}

@article {pmid41093016,
year = {2025},
author = {Jalili, C and Hosseinkhani, F and Dayer, D and Tabandeh, MR and Abbasi, A and Nasta, TZ},
title = {Indole-3-propionic acid Function through PXR and AhR, Molecular Signaling Pathways, and Antitoxic Role in Underlying Diseases.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106877},
doi = {10.1016/j.jsbmb.2025.106877},
pmid = {41093016},
issn = {1879-1220},
abstract = {The host organism's balance within the body relies on its crucial symbiotic relationship with gut microbiota. This balance, known as homeostasis, can be influenced by various factors. One significant factor is the role of bacterial metabolites from different substrates, such as tryptophan. Recent research has revealed that these metabolites impact many biological processes. Microbial metabolites, such as Indole-3-Propionic Acid (IPA), are produced by the intestinal microbiota by converting dietary tryptophan. IPA is absorbed by intestinal epithelial cells, transported via the portal circulation, undergoes minimal hepatic metabolism, and is subsequently released into the systemic circulation to reach peripheral tissues and exert its biological effects. The Pregnane X receptor (PXR) and aryl hydrocarbon receptor (AhR) are the two main receptors of IPA which induce different gene expression profiles and subsequently diverse biological pathways in different tissues. Once absorbed by intestinal epithelial cells, IPA is released into the circulatory system and can significantly affect the immune, cardiovascular, nervous, and gastrointestinal systems. Furthermore, IPA has been found to have positive effects on a cellular level by inhibiting oxidative stress injury and preventing the synthesis of proinflammatory cytokines. Numerous studies have highlighted IPA's antioxidant, anti-inflammatory, anti-cancer, and neuroprotective effects. Therefore, dysbiosis of IPA contributes to disorders such as metabolic syndromes, inflammatory conditions, cancer, and neuropsychiatric diseases. This review provides a detailed examination of the most recent studies on indole-3-propionic acid function through PXR and AhR, outlining its molecular signaling pathways and correlation with various diseases.},
}

@article {pmid41092906,
year = {2025},
author = {Wu, L and Li, Y and Wang, W and Deng, L and Ge, H and Cui, M and Bi, N},
title = {Gut microbiota predictive of the efficacy of consolidation immunotherapy and chemoradiotherapy toxicity in lung cancer.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100877},
doi = {10.1016/j.medj.2025.100877},
pmid = {41092906},
issn = {2666-6340},
abstract = {BACKGROUND: Gut microbiota (GM) predict responses to immune checkpoint inhibitors (ICIs) in patients with advanced lung cancer. However, its role in patients with locally advanced lung cancer undergoing chemoradiotherapy (CRT) combined with consolidation ICIs remains unclear.

METHODS: A total of 177 fecal samples were collected pre- and post-CRT. Using 16S ribosomal RNA (16S rRNA) sequencing and metagenomic data from an internal cohort and published studies, the kinetics of microbiota were analyzed using the Wilcoxon signed-rank test, while prognostic factors for progression-free survival (PFS) were identified using Cox regression modeling and machine learning algorithms.

FINDINGS: The GM configuration was unaffected by traditional CRT. However, in cases of CRT with consolidation ICIs, patients with long-PFS showed a higher alpha diversity at baseline, followed by a reduction during treatment, contrasting with the stable diversity observed in the short-PFS group. Enrichment of the symbiotic microbe Akkermansia muciniphila (Akk) after CRT was observed, with its increased abundance correlating with extended distant metastasis-free survival in patients undergoing CRT with consolidation ICIs. Notably, the trend in Akk variation was a prognostic indicator of survival outcomes in patients undergoing CRT combined with ICIs. GM was also involved in the development of treatment-related pneumonia and was a promising predictive marker for severe pneumonia.

CONCLUSIONS: CRT with consolidation ICIs has more pronounced effects on the GM than CRT alone in patients with locally advanced lung cancer. The dynamic variation in Akk has predictive potential for patient survival in this context.

FUNDING: This study was supported by the National Science and Technology Major Project.},
}

@article {pmid41092274,
year = {2025},
author = {Batnini, M and Kumar, A},
title = {Nutrient-symbiosis cross talk links phosphate starvation signaling with nodulation control.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf133},
pmid = {41092274},
issn = {1471-9053},
}

@article {pmid41090560,
year = {2025},
author = {Tian, YF and Luo, Y and Li, QM and Zhang, ZQ and Guo, YL and Yang, WC},
title = {CPOP1 is a key enzyme required for nodule microenvironment control and successful symbiotic nitrogen fixation in Lotus japonicus.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70037},
pmid = {41090560},
issn = {1744-7909},
support = {2023YFD1200605//National Key Research and Development Program of China/ ; 2016YFA0500500//National Key Research and Development Program of China/ ; 2023ZD04068//National Key Research and Development Program of China/ ; YSBR-011//CAS Project for Young Scientists in Basic Research/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Symbiotic nitrogen fixation in legumes requires the exquisite regulation of the environment within the infected region of the nodule. The microaerobic environment critical for nitrogenase activity is maintained through the physical oxygen diffusion barrier of the cortex and locally the oxygen-binding protein leghemoglobin (Lb). Leghemoglobin binds and releases oxygen with heme moiety to maintain oxygen gradients inside the infected cell (IC) during nitrogen fixation. Heme binds to diverse proteins and plays critical roles in different redox reactions. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation are not clear. Here, we identified coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme biosynthesis in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The IC-specific expression of CPOP1 was directed by the -881 to -740 bp promoter region. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild-type. Intriguingly, bacteria proliferation is inhibited due to the down-regulation of cell division-related gene expression upon CPOP1 knockout. Our data showed that CPOP1 is essential for the microaerobic environment control of ICs and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.},
}

@article {pmid41089933,
year = {2025},
author = {Song, Y and Xu, X and Xie, M and Tao, J and Jin, H and Liu, Y and Liu, L and Song, X and Meng, S and Cheong, IH and Wang, Y and Wei, Q},
title = {The lung microbiome in patients with HIV complicated with community-acquired pneumonia: a cross-sectional pilot study.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100480},
pmid = {41089933},
issn = {2666-5174},
abstract = {BACKGROUND: The composition of lung flora in HIV-combined community-acquired pneumonia (CAP) populations may be associated with the duration and severity of the disease. Additionally, a correlation may exist between lung flora balance and the body's autoimmune status. However, the number of studies in this area is limited. Therefore, we collected alveolar lavage fluid from 110 HIV-positive CAP patients at Beijing Ditan Hospital. We preliminarily explored the lung flora of this population using 16S amplicon analysis, and found some clues about the relationship between flora and immune status by comparing the flora of two groups of people with different immune status.

RESULTS: We found that the lung microbiome of HIV patients with CAP exhibited a "high-level aggregation-low-level dispersion" pattern across taxonomic hierarchies, this was characterised by dominant taxa at higher classification levels and dispersed, low-abundant taxa at lower levels. Microbial diversity in the AIDS group (CD4[+] counts < 200 cells/μL) was marginally lower than in the HIV group, but the difference was not statistically significant. The AIDS group exhibited increased relative abundances of pathogenic taxa (Gammaproteobacteria, Fusobacteriia) and decreased relative abundances of symbiotic taxa (Bacilli, Cyanobacteriia). LEfSe revealed significant enrichment of oral- and gut-associated microbial communities in the HIV group, as opposed to pathogen-enriched communities in the AIDS group. Microbial network analysis showed enhanced modularization in the AIDS group, with reduced clustering coefficients and network density, indicating destabilized microbial communities. Immune collapse appeared to drive a shift from cooperative hub-based to competitive modular microbial structures.

CONCLUSIONS: Immune status profoundly influenced the composition and function of the pulmonary microbiome in HIV infection. AIDS patients exhibited pathogen-dominated, less stable microbial communities. These findings provided foundational insights into interactions among HIV, CAP, and the pulmonary microbiome, and informed the development of microbiome-targeted interventions.},
}

@article {pmid41088742,
year = {2025},
author = {Lyu, X and Liu, K and Guo, T and Wang, X and Gong, Z and Ma, C},
title = {Nitrogen Fertilization Modulates Soybean Nodulation and Nitrogen Fixation via NO-Mediated S-Nitrosylation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11100},
pmid = {41088742},
issn = {1520-5118},
abstract = {Soybean, a symbiotic nitrogen-fixing crop, experiences suppressed nodule nitrogen fixation under excessive nitrogen fertilizer. Nitric oxide (NO) is a key signaling molecule regulating development and stress, primarily via protein S-nitrosylation, although its role in soybeans is unclear. Using a unilateral nodulation system, treatments with nitrogen, an NO scavenger, and an NO donor were applied. Results showed that nitrogen application increased the NO content in the nodules and reduced the nitrogen fixation capacity. Conversely, the NO scavenger lowered the NO levels but enhanced fixation. Exogenous NO inhibited fixation by damaging the nodule structure, reducing leghemoglobin, and disrupting NO homeostasis. Quantitative proteomics with iodoTMT labeling identified 287 S-nitrosylation sites on 238 nodule proteins. Nitrogen-altered proteins were involved in nitrogenase activity, stress response, and ABC transporters. This study establishes the 'nitrogen level-NO signal-S-nitrosylation-nodule function' pathway, offering molecular insights into S-nitrosylation's role in nodule regulation.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects

@article {pmid41086923,
year = {2025},
author = {Liang, Y and Yu, J and Yao, Z and Sun, Y and Feng, J and Shen, R and Luo, J and Zhao, L},
title = {Decoding microbial interactions: Interaction networks and regulatory strategies for medium-chain fatty acid biosynthesis through anaerobic chain elongation.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108735},
doi = {10.1016/j.biotechadv.2025.108735},
pmid = {41086923},
issn = {1873-1899},
abstract = {The anaerobic biosynthesis of medium-chain fatty acids (MCFAs) as valorized bio-based chemicals relies on intricate and dynamic interaction networks within microbial communities. This review systematically summarizes the key mechanisms and regulatory strategies driving MCFA biosynthesis in terms of microbial interactions, with a focus on electron donor-acceptor generation and chain elongation (CE) processes. The functional stability and resilience of anaerobic fermentation systems are collectively sustained by microbial diversity via modular functional partitioning, metabolic complementarity, resilience against perturbations, and environmental adaptation. Notably, substrate competition and syntrophic symbiosis between functional taxa directly govern the directionality and efficiency of the metabolic flux. Carbon source preferences and environmental factors synergistically steer pathway selection, while exogenous interventions such as enhanced electron transfer or niche occupation optimize microbial cooperation. In addition, quorum sensing and electrochemical synergy further balance inter-species competition to achieve a dynamic equilibrium between metabolic branch inhibition and enrichment of CE consortia. These multidimensional interaction mechanisms provide high-purity electron donors and stable metabolic foundations for MCFA synthesis to guide directional microbial engineering strategies to enhance product yields. This study systematically summarized how microbial interaction networks drive efficient MCFA biosynthesis via a multi-scale coordination between various mechanisms, including metabolic flux partitioning control, environmental response feedback, and functional modularization design, providing a theoretical foundation for resolving critical challenges during anaerobic MCFA fermentation.},
}

@article {pmid41086911,
year = {2025},
author = {Tu, C and Fan, R and Wu, Y and Liu, F and Xiao, W and Ziyodillo Ugli, OI and Qiong, Z and Peng, Y and Liu, J and Xu, F and Zhu, Y},
title = {Ultra-low concentrations of a botanical insecticide blend alter microbiota composition and gene expression in the ladybeetle Propylea japonica.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127252},
doi = {10.1016/j.envpol.2025.127252},
pmid = {41086911},
issn = {1873-6424},
abstract = {Botanical pesticides are increasingly promoted as environmentally benign alternatives to synthetic chemicals in integrated pest management. However, the ecological safety of their persistent ultra-low residues remains poorly understood, particularly regarding non-target natural predators. In this study, we investigated the chronic toxicological effects of an ultra-low concentration (ULC; 1/100 of LC30 of 15.106 mg/mL) of a botanical pesticide mixture-composed of commercially available tea saponin and matrine mixed at a ratio of 10:1 (v:v)-on the generalist Propylea japonica. Long-term exposure significantly prolonged larval development, reduced pupal mass, and compromised female fecundity, indicating potential disruptions to population stability and biocontrol efficacy. Gene expression analyses revealed stage-specific alterations in detoxification and hormone-related pathways: fourth-instar larvae exhibited elevated expression of GST and DuoX, downregulation of JHAMT1 and PjIRS1, and upregulation of EcR, whereas adult females showed marked suppression of JHDK, FOXO, PjIRS1, and Vg. These changes point to endocrine disruption and impaired reproductive capacity. Moreover, 16S rRNA sequencing revealed that ULC exposure significantly decreased microbial diversity and altered symbiont composition, particularly in adult beetles. Collectively, our findings demonstrate that even ultra-low residues of botanical pesticides can impose sublethal physiological stress and reshape symbiotic microbial communities in beneficial insects. This work underscores the need for refined ecological risk assessments of green pesticides and advocates for pest management strategies that balance effective control with the conservation of natural enemies.},
}

@article {pmid41086499,
year = {2025},
author = {Li, Y and Zheng, X and He, H and Hu, R and Han, Z and Tao, J and Lin, T and Chen, W},
title = {Microalgal-bacterial granular sludge enhances oxytetracycline removal: Microbial responses, degradation pathways, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140103},
doi = {10.1016/j.jhazmat.2025.140103},
pmid = {41086499},
issn = {1873-3336},
abstract = {Oxytetracycline (OTC), an emerging "low-concentration, high-toxicity" contaminant, presents considerable hurdles to wastewater treatment processes. This study systematically evaluated for the first time the impacts of OTC on the operational performance, sludge characteristics, and microbial metabolic activity across three treatment systems: microalgal-bacterial granular sludge (MBGS), aerobic granular sludge (AGS), and activated sludge (AS). Results demonstrated that MBGS exhibited superior treatment efficiency, maintaining stable removal of 500 μg/L OTC at 88.06 ± 1.45 % (p < 0.05). MBGS adapted to OTC exposure by increasing ATP content and reducing lactate dehydrogenase release. Acclimated MBGS primarily removed OTC through biodegradation. Moreover, multiple OTC transformation products with reduced toxic potential were detected, signifying that MBGS systems achieve efficient microbial degradation. Metagenomic analyses revealed that Pseudomonadota in MBGS displayed high adaptability under OTC exposure. Additionally, OTC exposure upregulated carbohydrate and energy metabolism in MBGS, thereby enhancing overall microbial metabolic activity. Alphaproteobacteria contributed most significantly to key functional genes, underscoring their critical role in contaminant removal in the MBGS. Redundancy analysis highlights a robust association between Alphaproteobacteria and the abundance of antibiotic resistance genes. This study confirms the MBGS's resilience to OTC-contaminated wastewater, highlighting its potential for efficient antibiotic wastewater treatment.},
}

@article {pmid41086179,
year = {2025},
author = {Ding, M and Liu, H},
title = {Spatiotemporal coupling and coordinated development of rural revitalization and rural tourism in Jiangsu.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0334241},
doi = {10.1371/journal.pone.0334241},
pmid = {41086179},
issn = {1932-6203},
mesh = {*Rural Population/statistics & numerical data ; China ; Humans ; *Tourism ; Spatio-Temporal Analysis ; },
abstract = {Rural tourism is pivotal in addressing the unidirectional urban-to-rural flow of resources, such as labor migration. However, the interaction between rural tourism and rural revitalization in developed regions remains poorly understood. This study establishes an evaluation index system for rural revitalization and rural tourism, examining their interrelationship. Using the entropy method and coupling coordination degree model, we assess the development levels and coordination degrees of these aspects in Jiangsu Province from 2012 to 2023. Furthermore, the geographical detector model is utilized to pinpoint the primary drivers influencing this coordination. The findings are: (1) Both rural revitalization and tourism exhibit significant growth, with southern Jiangsu outperforming the north; (2) The coupling coordination between these systems has strengthened, indicating a profound symbiotic relationship; (3) Spatial distribution differences are notable, with the coupling coordination degree D value in southern Jiangsu being 26.4% higher than in the north. This disparity is primarily attributable to the wider urban-rural income gap and greater fiscal investment in southern Jiangsu. Notably, the traditional "resource dependence theory" appears ineffective in Jiangsu, as the density of rural tourism resources is relatively low. Accordingly, the study proposes differentiated policy recommendations: northern Jiangsu should focus on talent attraction and the integration of culture and tourism, while southern Jiangsu should explore mechanisms to facilitate the two-way flow of urban-rural elements. This research provides a theoretical framework for coordinating "policy-market" dynamics in the rural transformation of developed regions.},
}

*Rural Population/statistics & numerical data
China
Humans
*Tourism
Spatio-Temporal Analysis

@article {pmid41085894,
year = {2025},
author = {Menaa, B and Ribeiro, I and Oliveira, M and Rahal, S and Carvalho, MF and Chekireb, D},
title = {Isolation and characterization of endophytic actinobacteria associated with Artemisia judaica L. ssp. sahariensis from desert regions in Algeria.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41085894},
issn = {1678-4405},
abstract = {Endophytic actinobacteria, known for symbiotic relationships with plants and production of bioactive compounds, occur in diverse environments, including deserts. The Sahara's nutrient scarcity, high temperatures, and salinity drive unique microbial adaptations, making it a promising reservoir of novel taxa. This study reports, for the first time, the isolation and characterization of endophytic actinobacteria from Artemisia judaica L. ssp. sahariensis, a medicinal plant of the Algerian desert. Forty-two actinobacterial isolates were obtained from root and leaf tissues and identified through 16 S rRNA gene sequencing, revealing their affiliation with five genera: Micromonospora, Nonomuraea, Nocardiopsis, Gordonia, and predominantly Streptomyces. These isolates were characterized for morphological, physiological, and bioactive traits, including stress tolerance, phosphate solubilization, extracellular enzyme production, and antibacterial activity. More than 93% exhibited antagonistic effects against at least one tested pathogen. The most active strains showed minimum inhibitory concentration values between 4 and 8 µg/mL, highlighting their strong antibacterial potential. All isolates tolerated up to 5% NaCl, and several, including AJR36, AJR38, and AJR16, grew at 15%. Phosphate solubilization was observed in 36% of isolates, while 38% displayed diverse enzymatic activities. Although this study focused on a single plant species, the observed functional diversity underscores the biotechnological potential of these desert-associated endophytes. These findings suggest that unexplored desert ecosystems harbor valuable Actinomycetota resources, supporting further investigations for the discovery of novel species and their potential applications in agriculture and medicine.},
}

@article {pmid41084897,
year = {2025},
author = {Desai, V and Sharma, AK and Chauhan, P},
title = {Endophytes and Plants Interaction: A Hidden Microbial World Inside the Plant.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70112},
doi = {10.1002/jobm.70112},
pmid = {41084897},
issn = {1521-4028},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Endophytes are a diverse group of microbes that colonize internal plant tissues without causing harm to the host. They play a crucial role in plant growth, development, and stress management. The is a complex mechanism involving evasive strategies to bypass host immune response, significant alteration in plant gene expression and establishment of a balance mutualistic relationship. Endophytes enhance plant health through various direct and indirect mechanisms, including the production of phytohormones such as auxin, gibberellins, and cytokinin. Moreover, they also solubilize nutrients, mainly nitrogen and phosphorus. A significant contribution of endophytes is the induction of induced systemic resistance (ISR), a defense response that primes the plant against a broad spectrum of pathogens and environmental stressors. The colonization of endophytes is governed by complex signaling pathways, immune modulation and tissue specificity, influenced by host genotype, age, and environmental conditions. This review highlights the ecological significance, mechanisms of colonization and functional contribution of endophytes to host plants. Furthermore, the review emphasizes that endophytes can recruit or influence other beneficial microbes in the rhizosphere region of host plants. Conclusively, this review synthesizes current understanding of the molecular strategies these microbes employ to survive within plant tissue and modulate plant immune system. We emphasize the immense, yet underexploited, potential of endophytes in enhancing plant resilience and productivity and advocates further research into their mechanisms and applications to meet growing demands of global agriculture.},
}

@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Symbiosis
Phylogeny
Metagenome/genetics
*Evolution, Molecular
Biological Evolution

@article {pmid41083230,
year = {2025},
author = {Caiafa, MV and Kaminsky, L and Healy, R and Sheffer, LP and Willis, CB and Deitz, K and Richter, BS and Lemmond, BR and Borland, D and Roy, BA and Dawson, HA and Delevich, CA and Conery, JS and Warner, D and Caboň, M and Karlsen-Ayala, E and Grupe, AC and Kraisitudomsook, N and Reynolds, NK and Drechsler-Santos, ER and Truong, C and Corrales, A and Mujic, AB and Kennedy, PG and Jusino, MA and Swenie, RA and Noffsinger, CR and Grootmyers, D and Matheny, PB and Wilson, AW and Smith, ME},
title = {Think globally, barcode locally: nine years of macrofungi sampling reveals extensive biodiversity at the ordway-swisher biological station, a subtropical site in Florida.},
journal = {Fungal biology},
volume = {129},
number = {7},
pages = {101643},
doi = {10.1016/j.funbio.2025.101643},
pmid = {41083230},
issn = {1878-6146},
mesh = {Florida ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics/chemistry ; *Fungi/classification/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics/chemistry ; Phylogeny ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; },
abstract = {The Ordway-Swisher Biological Station (OSBS) is a 38-km[2] reserve owned by the University of Florida and is part of the National Ecological Observatory Network (NEON). The reserve contains several iconic Florida habitats, such as sandhill, mesic hammock, and scrubby flatwoods. While plants and animals have been extensively studied at OSBS, the fungi remain poorly known. Fungal inventories are critical to increase knowledge of both fungal diversity and species ranges, and thus to provide foundational data for a wide array of applications in ecology and resource management. Here, we present the results of a nine-year effort to collect, preserve, and DNA barcode the macrofungi at OSBS. This effort generated >1200 vouchered specimens and 984 ITS rDNA sequences, representing more than 546 species. Our sampling was dominated by Basidiomycota and revealed a high diversity of symbiotic ectomycorrhizal fungi, particularly species of Amanita, Cortinarius, and Russula. Sampling curves and both Chao1 and Jacknife1 richness estimators suggest that our DNA barcoding efforts captured only about half of the macrofungi species and that a more complete inventory would detect 897-1177 macrofungi species at OSBS. Our sampling found more species of macrofungi at OSBS than the known number of vertebrate animal species at the reserve and our estimates also suggest that there are likely more macrofungi species than plant species at OSBS. This study is the first comprehensive macrofungi inventory within a NEON site and highlights the importance of long-term monitoring to provide novel data on fungal diversity, community structure, conservation, biogeography, and taxonomy.},
}

Florida
*Biodiversity
*DNA Barcoding, Taxonomic
DNA, Fungal/genetics/chemistry
*Fungi/classification/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics/chemistry
Phylogeny
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry
Molecular Sequence Data

@article {pmid41082848,
year = {2025},
author = {Chu, W and Li, X and Li, P and Li, J and Wang, Z and Zhou, H and Yang, X and Chen, S and Zhou, M and Wang, S and Zheng, J and Chen, Y and Yu, Y and Tan, Z},
title = {Enhanced treatment of low C/N domestic wastewater in a membrane photobioreactor: Operational control of microalgal-bacterial symbiosis for synergistic pollutant and antibiotic resistance genes removal.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127398},
doi = {10.1016/j.jenvman.2025.127398},
pmid = {41082848},
issn = {1095-8630},
abstract = {Conventional wastewater treatment technologies face significant limitations, including high CO2 emissions, poor resource recovery, and growing challenges from emerging contaminants such as antibiotics and their associated antibiotic resistance genes (ARGs), which pose serious risks to aquatic ecosystems and public health. In response to these challenges and within the framework of China's carbon neutrality goals, this study developed a microalgae-activated sludge membrane photobioreactor (MPBR) to enable synergistic pollutant removal and resource recovery from low carbon-to-nitrogen (C/N) domestic wastewater. Under the optimized internal circulation flow rate of 13.5 m[3]/d, the MPBR system achieved high removal efficiencies for ammonia nitrogen (NH4[+]-N, 99.48 %), total nitrogen (TN, 72.89 %), chemical oxygen demand (COD, 63.20 %), and total phosphorus (TP, 80.37 %). Simultaneously, ARGs and mobile genetic elements (MGEs) were reduced by approximately one log, attributed to two primary mechanisms: (1) suppression of ARGs in the sludge zone through the regulation of drug-resistant bacterial populations, and (2) inhibition of horizontal gene transfer in the microalgal zone via nitrogen-driven suppression of ARGs host bacteria, as well as enhanced microalgae-bacteria co-metabolism and community optimization. Furthermore, the optimization of microalgae photosynthesis and nitrogen cycling, along with microbial cooperation under anoxic conditions, supported efficient nutrient recovery while maintaining low-carbon operation. This study offers a novel, carbon-efficient strategy for integrating wastewater purification with ARGs risk mitigation, contributing to sustainable water management aligned with the circular economy and carbon neutrality objectives.},
}

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41081965,
year = {2025},
author = {Xu, L and Zhou, Y and Jin, X and Wang, Z and Song, Z and Zhang, X and Ding, H and Li, Y},
title = {Species diversity and drought tolerance of culturable dark septate endophytes in Anemone tomentosa in the Taihang mountain area.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {59},
pmid = {41081965},
issn = {1432-1890},
support = {HBCT2025190206//Innovation Team on Dry Fruits of Hebei Provincial Modern Agricultural Industry Technology System/ ; 2020YFD1000700//National Key R&D Program of China/ ; LC2025-08//Expert Support Team Project for Forest, Fruit and Flower Industry in Hebei Province/ ; 21326802D//Hebei Science and Technology Support Project/ ; },
mesh = {*Endophytes/physiology/classification ; *Droughts ; *Biodiversity ; *Anemone/microbiology/physiology ; China ; Soil Microbiology ; Plant Roots/microbiology ; Symbiosis ; Stress, Physiological ; Drought Resistance ; },
abstract = {Frequent drought events pose escalating threats to global ecosystems, driving vegetation degradation, biodiversity loss, while destabilizing ecosystem functions. Dark septate endophytes (DSE), which exhibit drought stress tolerance in vitro and have the potential to enhance plant drought tolerance in arid environments, represent a key microbial component possibly mitigating drought impacts. Therefore, this study focuses on the dominant drought-tolerant plant Anemone tomentosa (A. tomentosa) and its symbiotic DSE in the drought-prone Taihang Mountain area, aiming to reveal the community composition, spatial distribution and functions of DSE, explore their application potential in arid environments, and provide a basis for fully utilizing DSE resources to promote vegetation restoration and ecological reconstruction in arid regions. Root and soil samples of A. tomentosa were collected from six sampling sites in the Taihang Mountain area to systematically investigate DSE colonization, community composition, species diversity and their correlations with soil environmental factors across different sites. Then six DSE strains with high isolation frequencies were selected for the drought resistance study in pure cultures, and varying polyethylene glycol (PEG-6000) concentrations (0%, 15%, 25%, And 35%) were set to simulate drought stress. The results showed that the roots of A. tomentosa at all six sampling sites in the Taihang Mountain area were highly colonized by DSE, forming typical dark-colored septate hyphae And microsclerotia structures. A total of 20 DSE strains belonging to 14 genera were isolated and identified, and the community composition of DSE at different sampling sites differed significantly (P < 0.05). The results of redundancy analysis (RDA) showed that soil organic carbon and soil total phosphorus were the Main factors influencing the community composition of DSE. The growth of 5 frequently isolated DSE strains under pure culture conditions was not adversely affected by drought stress, except for Exophiala xenobiotica (Ex), and biomass accumulation increased significantly with increasing drought stress, which was related to the content of antioxidant enzymes, osmotic adjustment substances, membrane lipid peroxidases and melanin in the different fungi. In summary, A. tomentosa in Taihang Mountain has rich DSE species diversity, and the two can form a symbiotic relationship, thus enhancing the adaptability of A. tomentosa to the environment. Five DSE strains exhibited drought stress tolerance under in vitro culture conditions, which enriched the understanding of the ecological functions and adaptive mechanisms of DSE in arid environments and provided a basis for the development and application of drought-resistant and water-preserving microbial agents.},
}

*Endophytes/physiology/classification
*Droughts
*Biodiversity
*Anemone/microbiology/physiology
China
Soil Microbiology
Plant Roots/microbiology
Symbiosis
Stress, Physiological
Drought Resistance

@article {pmid41081895,
year = {2025},
author = {Yamaoka, NK and Packard, EE and Jones, MD},
title = {Nitrogen accumulation accompanies ectomycorrhiza formation in pine germinants the first growing season after wildfire or clearcutting.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {58},
pmid = {41081895},
issn = {1432-1890},
support = {RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-03927//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Mycorrhizae/growth & development/physiology/metabolism ; *Nitrogen/metabolism ; *Pinus/microbiology/growth & development/metabolism ; Seasons ; Seedlings/microbiology/growth & development ; *Wildfires ; Plant Roots/microbiology ; Symbiosis ; Germination ; Ascomycota ; },
abstract = {Early stages of the ectomycorrhizal symbiosis have rarely been studied on seedlings germinating in the field. By collecting lodgepole and ponderosa pine seedlings during their first growing season in recent clearcuts and burned areas, we were able to identify when colonization of pine roots first began, the rate at which ectomycorrhizal fungi colonized new germinants, and how this related to nitrogen nutrition and growth. Pine seedlings were first colonized in July, a month after germination was first observed. As the first seedlings became mycorrhizal, ectomycorrhizal lodgepole pine seedlings contained approximately 40% more nitrogen and > 60% greater biomass compared to uncolonized seedlings collected at the same time. Nitrogen content was 47% higher in mycorrhizal than nonmycorrhizal naturally-regenerating ponderosa pine seedlings. Ascomycetes, with a Pustularia sp. and Wilcoxina spp. most abundant, formed 80% of the ectomycorrhizae. Because all collected seedlings had ectomycorrhizae present on their roots by the end of the season, we concluded that inoculum of ectomycorrhizal fungi, especially of ruderal ascomycetes, was not limiting colonization of seedlings on these severely burned or recently clearcut sites. Our results are consistent with a role for ectomycorrhizal fungi in nitrogen acquisition, even within the first weeks after mycorrhiza formation; however, it is also possible that larger, more nitrogen-replete seedlings became colonized earlier than smaller seedlings. We saw no evidence of nitrogen loss by mycorrhizal pine seedlings as observed in previous studies.},
}

*Mycorrhizae/growth & development/physiology/metabolism
*Nitrogen/metabolism
*Pinus/microbiology/growth & development/metabolism
Seasons
Seedlings/microbiology/growth & development
*Wildfires
Plant Roots/microbiology
Symbiosis
Germination
Ascomycota

@article {pmid41081502,
year = {2025},
author = {Castro-Camacho, V and Robles-Azor, R and Rodríguez-Burdock, L and Rojas-Jimenez, K and Mendoza-Guido, B},
title = {Draft genome sequence of Methylobacterium aquaticum LEGMi-203a, isolated from root nodules of Pithecellobium hymenaeifolium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0075425},
doi = {10.1128/mra.00754-25},
pmid = {41081502},
issn = {2576-098X},
abstract = {We report the draft genome of Methylobacterium aquaticum LEGMi-203a, a root nodule isolated from Pithecellobium hymenaeifolium. Genomic analysis supports its classification as M. aquaticum, and annotated nitrogen fixation and nodulation genes underscore its possible functional capabilities as a symbiont in tropical plants.},
}

@article {pmid41081364,
year = {2025},
author = {Barrinha, A and Loyola-Machado, AC and Mariano Dos Santos, MD and Carvalho, PC and de Souza, W and Valente, AP and Galina, A and Motta, MCM},
title = {Endosymbiosis in trypanosomatids: the bacterium regulates the intermediate and oxidative metabolism of the host cell.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0045725},
doi = {10.1128/msphere.00457-25},
pmid = {41081364},
issn = {2379-5042},
abstract = {UNLABELLED: Endosymbiosis in trypanosomatids involves a mutualistic association between a symbiotic bacterium and a host protozoan and represents an excellent model for studying metabolic coevolution and the origin of organelles. This work investigated the influence of the symbiont on the metabolism of Angomonas deanei by comparing wild-type and aposymbiotic strains under different nutritional conditions. The presence of the symbiont enhanced cell proliferation in the medium containing a single carbon source and increased O2 consumption. Wild-type cells utilized oxidative phosphorylation to produce ATP, whereas aposymbiotic cells relied on substrate-level glycolysis, resulting in the excretion of greater amounts of fermentative products, such as acetate, succinate, and ethanol. Proteomic analysis revealed an increased expression of glycolytic and fermentative enzymes by the aposymbiotic strain and oxidative phosphorylation enzymes by symbiont-harboring cells. These findings highlight the role of the symbiotic bacterium in optimizing host metabolism and provide insights into the evolution of parasitism in trypanosomatids when A. deanei is compared with pathogenic species.

IMPORTANCE: This work provides groundbreaking insights into the metabolic and evolutionary dynamics of endosymbiosis, a topic of central importance to cellular evolution. Angomonas deanei, a trypanosomatid species, has become a paradigm for investigating the evolution of eukaryotic cells and the origin of organelles through endosymbiosis. Harbored in the cytoplasm of this protozoan, the symbiont engages in intricate metabolic exchanges, offering a time window to analyze the processes and evolutionary history that underlie the establishment of permanent endosymbiotic relationships. By employing a multidisciplinary approach, we have uncovered how the symbiotic bacterium regulates the oxidative metabolism of the trypanosomatid, integrating glucose catabolism and optimizing energy production. Our discoveries have broad implications for understanding the metabolic integration of organelles, such as mitochondria and glycosomes, with the bacterial endosymbiont. Beyond unravelling the complexities of metabolic adaptations during symbiosis, our work may contribute to the general understanding of the evolutionary dynamics of parasitism within the Trypanosomatidae family.},
}

@article {pmid41080487,
year = {2025},
author = {Boyle, JA and Murphy, B and Teng, F and Babaei Zadeh, P and Ensminger, I and Stinchcombe, JR and Frederickson, ME},
title = {Mutualism Mediates Legume Response to Microbial Climate Legacies.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72271},
pmid = {41080487},
issn = {2045-7758},
abstract = {Climate change is altering both soil microbial communities and the ecological context of plant-microbe interactions. Heat, drought, and their legacies can alter soil microbiomes and potential plant symbionts, but the direct consequences of these microbial changes on plant performance and plant investment in symbiosis remain underexplored. Predicting how soil microbes modulate plant resilience to heat and drought is critical to mitigating the negative effects of climate change on ecosystems and agriculture. In this proof of concept study, we conducted growth chamber experiments to isolate the microbially mediated indirect effects of heat and drought on plant performance and symbiosis. In the first experiment, focused on drought, we found that drought and drought-treated microbes, along with their interaction, significantly decreased the biomass of Medicago lupulina plants compared to well-watered microbiomes and conditions. In a second experiment, we then tested how the addition of a well-known microbial mutualist, Sinorhizobium meliloti, affected heat- and drought-treated microbiomes' impact on M. lupulina. We found that drought-adapted microbiomes negatively impacted legume performance by increasing mortality and reducing branch number, but that adding rhizobia erased differences in plant responses to climate-treated soils. In contrast, heat-adapted microbiomes did not differ significantly from control microbiomes in their effects on a legume. Our results suggest microbial legacy effects, mutualist partners, and their interactions are important in mediating plant responses to drought, with some mutualists equalizing plant responses across microbial legacies.},
}

@article {pmid41080445,
year = {2025},
author = {Burchardt, S and Wojtaczka, P and Kućko, A and Ostrowski, M and Wilmowicz, E},
title = {Advancing 2-DE Techniques: High-Efficiency Protein Extraction From Lupine Roots.},
journal = {Bio-protocol},
volume = {15},
number = {19},
pages = {e5461},
pmid = {41080445},
issn = {2331-8325},
abstract = {Protein isolation combined with two-dimensional electrophoresis (2-DE) is a powerful technique for analyzing complex protein mixtures, enabling the simultaneous separation of thousands of proteins. This method involves two distinct steps: isoelectric focusing (IEF), which separates proteins based on their isoelectric points (pI), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), which separates proteins by their relative molecular weights. However, the success of 2-DE is highly dependent on the quality of the starting material. Isolating proteins from plant mature roots is challenging due to interfering compounds and a thick, lignin-rich cell wall. Bacterial proteins and metabolites further complicate extraction in legumes, which form symbiotic relationships with bacteria. Endogenous proteases can degrade proteins, and microbial contaminants may co-purify with plant proteins. Therefore, comparing extraction methods is essential to minimize contaminants, maximize yield, and preserve protein integrity. In this study, we compare two protein isolation techniques for lupine roots and optimize a protein precipitation protocol to enhance the yield for downstream proteomic analyses. The effectiveness of each method was evaluated based on the quality and resolution of 2-DE gel images. The optimized protocol provides a reliable platform for comparative proteomics and functional studies of lupine root responses to stress, e.g., drought or salinity, and symbiotic interactions with bacteria. Key features • Protocol tailored for isolating proteins from lupine roots, including those involved in symbiotic relationships with bacteria. • Our method is suitable for analyzing complex protein mixtures through IEF and SDS-PAGE for high-resolution separation. • Optimized precipitation method increases protein yield for downstream mass spectrometry and comparative proteomic analyses.},
}

@article {pmid41079636,
year = {2025},
author = {He, W and Wang, M and Zhong, Z and Chen, H and Xi, S and Zhang, H and Li, M and Sun, W and Zhang, Y and Wang, Y and Guo, X and Li, L and Du, Z and Luan, Z and Li, C and Zhang, X},
title = {In situ semi-quantitative imaging of intracellular metabolic interaction by confocal Raman microscopy.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113558},
pmid = {41079636},
issn = {2589-0042},
abstract = {Non-destructive subcellular metabolite quantification can reveal critical insights into biological interactions (e.g., endosymbiont-host crosstalk). Therefore, we developed a multivariate semi-quantitative imaging method using internal standardization to resolve simultaneous subcellular distributions of multiple metabolites, leveraging confocal Raman microscopy's (CRM's) high spatial resolution. The method was applied to the endosymbiotic mussel Gigantidas platifrons, whose symbiotic interaction mechanism has not been elucidated because symbionts cannot be cultivated. The results showed that the aggregated distribution of distinct phenotypes of symbiont strains was characterized by different glycogen abundances, indicating niche-driven metabolic strategies. Our data may provide direct evidence suggesting that symbionts supply intermediates to the host for cholesterol synthesis, potentially via vesicular trafficking. This work demonstrates CRM's capacity for comparative, spatially resolved metabolite quantification across cellular compartments. While semi-quantitative, CRM emerges as a powerful non-invasive tool for probing metabolic network dynamics and compartmentalization in challenging biological systems where traditional methods are limited.},
}

@article {pmid41077848,
year = {2025},
author = {Gao, JP and Kumar, A},
title = {RAM1-WRI Synergy: A GRAS-AP2 Regulatory Axis for Nutrient Exchange in Arbuscular Mycorrhizal Symbiosis.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70237},
pmid = {41077848},
issn = {1365-3040},
support = {//We would like to acknowledge finding support to Jin-Peng Gao by a grant to the University of Cambridge by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth and Development Office (grant no. OPP1028264) known as the Enabling Nutrient Symbioses in Agriculture (ENSA) project./ ; },
}

@article {pmid41077805,
year = {2025},
author = {Ma, C and Wu, C and Han, H and Bai, D and Zhang, Z and Li, Y and Wang, H},
title = {Metabolomics Reveals Concentration-Specific Adaptive Mechanisms of Arbuscular Mycorrhizal Fungi in Cadmium Translocation and Detoxification in Arundinoideae (Phragmites australis).},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70230},
pmid = {41077805},
issn = {1365-3040},
support = {//This study was funded by the National Natural Science Foundation of China (52070064, 42330705) and Science Research Project of Hebei Education Department (BJK2024161)./ ; },
abstract = {The symbiosis of arbuscular mycorrhizal fungi (AMF) and Phragmites australis (Pa) is an effective biological strategy for cadmium (Cd) remediation, however, the bioaccumulation and translocation mechanisms underlying this symbiosis remain underexplored. In this study, Cd and nutrient element concentrations in four Pa tissues were analyzed, along with ultrastructure observations and root metabolomics profiling, under different Cd concentrations (1 mg/L, 5 mg/L) and exposure durations (7 days, 30 days). The root metabolomics analysis, in combination with Cd accumulation patterns and ultrastructural observations, provided crucial insights into the biochemical pathways and molecular mechanisms involved in Cd detoxification, nutrient redistribution, and subcellular structural changes in the AMF-Pa symbiotic system. AMF reduced Cd accumulation in all Pa tissues under 1 mg/L Cd for 7 days and in roots under 5 mg/L Cd for 30 days. Conversely, with AMF, Pa accumulated more Cd in the other exposure groups. Under 5 mg/L Cd for 30 days, AMF facilitated Cd translocation from roots to aboveground parts. AMF altered Cu, Zn and P bioaccumulation in old roots and significantly influenced Fe accumulation in roots across all treatments. While 5 mg/L Cd disrupted cellular ultrastructure, AMF inoculation protected intracellular organ integrity and promoted cell wall thickening. This study reveals the dynamic mechanisms by which AMF regulate Cd translocation and accumulation under varying Cd concentrations. Under high Cd concentrations, AMF enhance energy metabolism and chelation, promoting Cd translocation from roots to aerial parts while mitigating Cd toxicity in the endodermis. In contrast, under low Cd concentrations, AMF suppress Cd uptake and promote its immobilization within root tissues by activating amino acid and nucleotide metabolism, reducing Cd translocation to aboveground parts. Additionally, AMF strengthen cell walls through phenylpropanoid biosynthesis, offering protection against Cd toxicity. These findings provide crucial theoretical insights for the application of AMF in phytoremediation of Cd-contaminated soils.},
}

@article {pmid41077488,
year = {2025},
author = {Ding, H and Li, X and Wang, S and Yang, Y and Chen, X and Chen, C and Wang, H},
title = {Trichoderma harzianum for the control of agricultural pests: Potential, progress, applications and future prospects.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.09.004},
pmid = {41077488},
issn = {0325-7541},
abstract = {This paper systematically reviews the taxonomic characteristics, pest control mechanisms, and field application cases of Trichoderma harzianum. As a non-toxic and environmentally friendly biocontrol fungus, T. harzianum exerts its pest control effects through various modes of action, including direct actions (such as parasitism, the production of insecticidal metabolites, and the release of antifeedant and repellent compounds) and indirect actions (such as inducing plants to enhance their resistance, attracting natural enemies of pests, and affecting insect symbiotic fungi). It can effectively control various agricultural pests, including nematodes and aphids. Moreover, the paper focuses on analyzing how modern formulation technologies (e.g., microencapsulation), synergistic strategies (in combination with biological and/or chemical agents), and genetic engineering enhance its biocontrol efficiency. This study aims to provide a theoretical basis and technical reference for constructing a sustainable pest management system based on T. harzianum, addressing pest control challenges within the context of increasing global food demand and supporting sustainable agricultural development.},
}

@article {pmid41077112,
year = {2025},
author = {Zonnequin, M and Vallet, M and Delage, L and Pohnert, G and Leblanc, C and Markov, GV},
title = {Differential impact of copper stress in two Ectocarpales: metabolic disruption and defensive signaling in the free-living Ectocarpus sp7 and the endophytic Laminarionema elsbetiae.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.10.006},
pmid = {41077112},
issn = {1638-6183},
abstract = {Algae are photosynthetic organisms, responsible for the primary production in oceans and lakes. Brown algae have evolved independently from other major eukaryotic lineages, such as the Opistokonts (animals, fungi) or Archaeplastida (land plants, green and red algae). Within this lineage, there is considerable variation between species, which differ in ecology, diversity, and evolutionary features, suggesting specific adaptations in their changing marine environment. In this context, several questions remain regarding the evolution of brown algal metabolism, particularly in response to oxidative stress. This study explored the consequences of copper stress on two brown algae from the Ectocarpales order: the free-living Ectocarpus sp7 and the endophytic Laminarionema elsbetiae. Using PAM-based fluorescence measurements, we revealed that high copper exposure reduces the photosynthetic capacity and activity of the endophyte. Through a cutting-edge untargeted metabolomic approach using UHPLC-HRMS profiling, we detected metabolic alterations induced by short-term exposure to moderate copper concentration in both free-living and endophytic Ectocarpales. The metabolite-regulated response appears to be substantial in Ectocarpus sp7 compared to L. elsbetiae, as a greater number of up- and down-regulated features were detected. Among the discriminant ions identified by tandem mass spectrometry, our results confirmed that copper exposure triggers the metabolism of algal defense signaling, primarily through the upregulation of oxylipins, but mainly in Ectocarpus sp 7. Altogether, our findings suggest that in Ectocarpales, fine metabolic adaptation may have altered the metabolism linked to defense signaling, such as the oxylipin pathway, particularly in ecological niches like endophytic life.},
}

@article {pmid41074950,
year = {2025},
author = {Zimmermann, F and Bouffaud, ML and Herrmann, S and Göttig, M and Graf, R and Tarkka, M and Opgenoorth, L and Croll, D and Peter, M and Dauphin, B},
title = {An ectomycorrhizal fungus alters developmental progression during endogenous rhythmic growth in pedunculate oak.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {57},
pmid = {41074950},
issn = {1432-1890},
mesh = {*Quercus/microbiology/growth & development ; *Mycorrhizae/physiology ; Symbiosis ; *Basidiomycota/physiology ; Plant Roots/microbiology/growth & development ; *Ascomycota/physiology ; Biomass ; },
abstract = {Pedunculate oak (Quercus robur L.), a long-lived forest tree species, forms symbiotic relationships with ectomycorrhizal (ECM) fungi, which can promote nutrient uptake, stress resilience, and growth. Like other tropical and temperate tree species, pedunculate oak exhibits endogenous rhythmic growth (ERG), a trait conferring the ability to repeatedly alternate root and shoot flushes as well as growth cessation as response to changing environmental conditions. However, the effects of different ECM fungal species on the ERG dynamics remain largely unknown. Here, we investigated the impact of two ECM fungi-Piloderma croceum, a basidiomycete previously shown to promote growth while not found in natural oak stands, and Cenococcum geophilum, an oak-native ascomycete with broad ecological range-on growth performance, biomass partitioning, and ERG patterns in a clonal oak system (clone DF159). By combining in vitro experiments with Bayesian modelling, we show that P. croceum promotes tree growth among treatments, without disrupting the endogenous growth rhythm. In contrast, C. geophilum, while showing high mycorrhization rates, led to reduced biomass accumulation and altered developmental progression through the ERG stages, especially by prolonging the steady state development stage-part of the root flush and characterized by peak net carbon assimilation. Co-inoculation revealed a competitive advantage of C. geophilum in root colonization, yet growth responses resembled those of the control. Our findings demonstrate that ECM species exert species-specific effects on biomass production and temporal development of plants, underscoring the functional importance of ECM fungi in shaping host development. Assessing these interactions provides new insights into the functional diversity of ectomycorrhizal symbiosis and can inform forest management strategies aimed at enhanced resilience in oak-dominated ecosystems under rapidly changing climatic conditions.},
}

*Quercus/microbiology/growth & development
*Mycorrhizae/physiology
Symbiosis
*Basidiomycota/physiology
Plant Roots/microbiology/growth & development
*Ascomycota/physiology
Biomass

@article {pmid41072151,
year = {2025},
author = {Zhou, Y and Man, XY},
title = {The epidermal immune microenvironment plays a central role in the pathogenesis of psoriasis.},
journal = {Current opinion in immunology},
volume = {97},
number = {},
pages = {102674},
doi = {10.1016/j.coi.2025.102674},
pmid = {41072151},
issn = {1879-0372},
abstract = {Psoriasis is a chronic immune-mediated skin disease whose inflammation can affect other systems and lead to various comorbidities. As a model inflammatory skin disease, while advances in mechanistic insights and targeted therapies have improved outcomes, unmet clinical needs persist. Modern technologies like single-cell sequencing and spatial transcriptomics reveal that skin immunity operates as a complex network involving neuroregulation, symbiotic microbial immunity, metabolic abnormalities, and reprogramming. These findings underscore the complexity of the local immune microenvironment in the skin and its central role in disease pathogenesis. In psoriatic inflammation, the epidermal immune microenvironment - driven by keratinocytes, dendritic cells, T cells, and skin microbiota - emerges as a core pathogenic mechanism. Keratinocytes, acting as both inflammatory effectors and disease drivers, interact with immune cells to initiate and amplify responses. Studying this microenvironment offers novel therapeutic targets for psoriasis and related inflammatory skin diseases.},
}

@article {pmid41070750,
year = {2025},
author = {Seah, BKB},
title = {Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {6},
pages = {e70049},
doi = {10.1111/jeu.70049},
pmid = {41070750},
issn = {1550-7408},
mesh = {*Symbiosis ; *Eukaryota/physiology/classification/genetics ; *Knowledge Bases ; *Archaea/physiology/genetics ; *Databases, Factual ; *Prokaryotic Cells/physiology ; *Bacteria/genetics/classification ; Software ; },
abstract = {As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here I present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 1146 manually curated interaction statements sourced from 443 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy, and Gene Ontology. I describe how its data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.},
}

*Symbiosis
*Eukaryota/physiology/classification/genetics
*Knowledge Bases
*Archaea/physiology/genetics
*Databases, Factual
*Prokaryotic Cells/physiology
*Bacteria/genetics/classification
Software

@article {pmid41068596,
year = {2025},
author = {Torrescassana, EC and Del Carmen Montero-Calasanz, M and Knight, M and Stach, J and Howard, TP},
title = {Genomic and functional analyses reveal Pseudomonas granadensis CT364 is a plant growth-promoting endophyte.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {651},
pmid = {41068596},
issn = {1471-2180},
support = {BB/T008695/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RYC2019-028468-I//Ramón y Cajal Research Grant, Spanish Ministry of Economy, Industry and Competitiveness/ ; },
mesh = {*Endophytes/genetics/physiology/isolation & purification ; *Pseudomonas/genetics/physiology/isolation & purification/classification ; Rhizosphere ; Plant Roots/microbiology/growth & development ; Genome, Bacterial ; *Plant Development ; Genomics ; Soil Microbiology ; Olea/microbiology/growth & development ; Arabidopsis/microbiology/growth & development ; Biofilms/growth & development ; },
abstract = {BACKGROUND: Plant-associated endophytes offer promising agricultural, environmental, and biotechnological applications. Despite their potential utility, difficulties in culturing these microorganisms under laboratory conditions have limited both their isolation and a comprehensive understanding of their biology, function, and ecological role. Against this background, Pseudomonas granadensis strain CT364-isolated from the olive tree rhizosphere-emerged as a potential endophyte of interest due to its cultivability and its ability to promote rooting across diverse species, including olive trees, rapeseed, mung bean and cowpea.

RESULTS: Genome Annotation and in silico predictions identified 564 genes linked to rhizosphere competence, plant colonisation and plant growth-promoting traits. Experimental findings confirmed the strain's motility, capacity for biofilm formation, and ability to sense and respond to plant-derived signals. P. granadensis CT364 effectively colonises the rhizosphere, rhizoplane, and internal tissues of Arabidopsis, confirming its endophytic nature without exhibiting any pathogenic traits. Inoculation experiments demonstrated significant effects on root architecture and increases in plant biomass and rosette area. Notably, these benefits were retained under salinity and osmotic stress, underscoring its plant growth-promoting ability. Finally, both genome analysis and experimental tests confirmed its resistance to osmotic stress and heavy metal toxicity, highlighting the strain's ability to survive in difficult environments.

CONCLUSIONS: The integration of genomic insights and experimental validation supports the conclusion that P. granadensis CT364 is a plant growth-promoting endophytic bacterium. Its ability to enhance plant development under both optimal and stressful conditions, combined with its ability to colonise Arabidopsis and non-pathogenic nature, positions this strain as a potential bioinoculant for sustainable agriculture. Furthermore, the identification of specific genes related to plant sensing and colonisation, and its genetic tractability, open avenues for exploring underlying mechanisms of plant-microbe interactions. In summary, P. granadensis CT364 therefore not only holds potential for improving crop performance under challenging environmental conditions but also offers a valuable model for the study of beneficial plant-bacterial symbiosis.},
}

*Endophytes/genetics/physiology/isolation & purification
*Pseudomonas/genetics/physiology/isolation & purification/classification
Rhizosphere
Plant Roots/microbiology/growth & development
Genome, Bacterial
*Plant Development
Genomics
Soil Microbiology
Olea/microbiology/growth & development
Arabidopsis/microbiology/growth & development
Biofilms/growth & development

@article {pmid41068135,
year = {2025},
author = {Cleveland, D and Nayak, R and Joseph, F and Nguyen, TA},
title = {Characterization of sustainable bacterial cellulose from Indigenous Vietnamese biomass for potential textile applications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35267},
pmid = {41068135},
issn = {2045-2322},
support = {IRG2022/1//RMIT International University/ ; },
mesh = {*Cellulose/chemistry/metabolism ; *Textiles/microbiology ; *Biomass ; Spectroscopy, Fourier Transform Infrared ; Vietnam ; *Bacteria/metabolism ; Microscopy, Electron, Scanning ; Calorimetry, Differential Scanning ; *Acetobacter/metabolism/chemistry ; },
abstract = {This research explored the fabrication and characterization of bacterial cellulose (BC), with a distinct emphasis on leveraging indigenous Vietnamese biomass sources. A diverse sample library consisting of 150 BC samples was prepared, with six samples selected for objective evaluation, based on the standard test methods. These samples were subjected to characterization techniques including Scanning electron microscopy (SEM), Energy dispersive X-ray (EDX), Fourier Transformation Infrared (FTIR) and Differential scanning calorimetry (DSC) to explore potential applications of BC in fashion and textiles. Moreover, the growth medium (or SCOBY- Symbiotic Culture of Bacteria and Yeast), from which the BC was cultivated, was analyzed to identify the constituent bacterial and yeast strains. The EDX analysis showed the major elements of BC were Carbon (C) followed by Oxygen (O), which accounted for 99% of the elemental composition of BC. The cellulosic structure was confirmed by the FTIR results, which indicated the characteristics bonds of BC. The DSC results showed that thermal stability can be achieved for the fashion and textiles produced from BC. Bacterial analysis showed the presence of Acetobacter Indonesiensis, a gram-negative bacterium, in all the BC samples. The outcomes of this study established a deeper comprehension of the morphological, thermal, biological, and chemical attributes of BC, as well as the microbial dynamics within the SCOBY mother. This exploration not only augments the existing knowledge on BC's potential in material design but also paves the way for further research on the influence of local ingredients on biomaterial production, thereby contributing to the burgeoning field of sustainable material innovation within a localized context.},
}

*Cellulose/chemistry/metabolism
*Textiles/microbiology
*Biomass
Spectroscopy, Fourier Transform Infrared
Vietnam
*Bacteria/metabolism
Microscopy, Electron, Scanning
Calorimetry, Differential Scanning
*Acetobacter/metabolism/chemistry

@article {pmid41066987,
year = {2025},
author = {Zhang, C and Zhang, Y and Diao, G and Hou, N and Zhao, X and Li, D},
title = {Decoding pyrene-induced reactive oxygen species production in the rhizosphere and their role in biodegradation: The repair mechanism of symbiotic driving by Fe(II) and microorganisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140073},
doi = {10.1016/j.jhazmat.2025.140073},
pmid = {41066987},
issn = {1873-3336},
abstract = {Reactive oxygen species (ROS) are considered key drivers of biogeochemical processes. However, there is limited research on the factors influencing ROS generation in the rhizosphere due to polycyclic aromatic hydrocarbon (PAHs) pollution during plant-microbe joint remediation, as well as their role in biodegradation. This study demonstrated that exposure to pyrene at a concentration of 100 mg/kg significantly enhanced the release of hydrogen peroxide (H2O2), hydroxyl radicals (•OH), and superoxide anions (O2•[-]) in the rhizosphere of ryegrass during root development. The concentrations of these reactive oxygen species were 1.5-7.8 times higher than those in the control group. Additionally, the Fe(II) concentration increased by 37.5 ± 3.2 %, and the pyrene degradation rate reached 26.8 ± 1.4 %. These results indicate that pyrene serves as a major factor stimulating ROS generation in ryegrass. Among these processes, Fe(II) catalyzes the production of •OH, which directly attacks the benzene ring structure of pyrene. High-throughput analysis further revealed that ROS enhanced the diversity, cohesion, and robustness of the rhizosphere microbial community structure. Furthermore, Pseudomonas, Marmoricola, Nocardioides and Dietzia were identified as core microbial genera involved in pyrene degradation and ecological restoration. Metagenomics analysis suggests that rhizosphere microorganisms respond to ROS-induced oxidative stress by enhancing ATP synthesis, which provides energy for antioxidant-related protein production and damage repair, thereby accelerating pyrene degradation. These results elucidate the ROS-mediated driving mechanism behind microbial pyrene degradation in plant-microbe combined remediation systems, thereby providing a theoretical basis for optimizing bioremediation strategies for organically contaminated soils.},
}

@article {pmid41066576,
year = {2025},
author = {Frison, M and Lockey, BS and Nie, Y and Golder, Z and Theiaspra, E and Ryall, CD and Lyons, C and Burr, SP and Prater, M and Bozhilova, LV and Glynos, A and Stewart, JB and Jones, NS and Chiaratti, MR and Chinnery, PF},
title = {Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6769},
pages = {156-163},
doi = {10.1126/science.adr5438},
pmid = {41066576},
issn = {1095-9203},
mesh = {*Mitophagy/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Mice ; *Mutation ; *Mitochondria/genetics/metabolism ; *Ubiquitin/metabolism ; Heteroplasmy ; Humans ; *Thiolester Hydrolases/metabolism/antagonists & inhibitors/genetics ; Proteasome Endopeptidase Complex/metabolism ; Mitochondrial Diseases/genetics ; Zygote ; Female ; },
abstract = {Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as fast as the nuclear genome, challenging this symbiotic relationship. Mechanisms must have evolved to moderate the impact of mtDNA mutagenesis but are poorly understood. Here, we observed purifying selection of a mouse mtDNA mutation modulated by Ubiquitin-specific peptidase 30 (Usp30) during the maternal-zygotic transition. In vitro, Usp30 inhibition recapitulated these findings by increasing ubiquitin-mediated mitochondrial autophagy (mitophagy). We also found that high mutant burden, or heteroplasmy, impairs the ubiquitin-proteasome system, explaining how mutations can evade quality control to cause disease. Inhibiting USP30 unleashes latent mitophagy, reducing mutant mtDNA in high-heteroplasmy cells. These findings suggest a potential strategy to prevent mitochondrial disorders.},
}

*Mitophagy/genetics
Animals
*DNA, Mitochondrial/genetics
Mice
*Mutation
*Mitochondria/genetics/metabolism
*Ubiquitin/metabolism
Heteroplasmy
Humans
*Thiolester Hydrolases/metabolism/antagonists & inhibitors/genetics
Proteasome Endopeptidase Complex/metabolism
Mitochondrial Diseases/genetics
Zygote
Female

@article {pmid41066235,
year = {2025},
author = {Kaur, R and Kalra, M and Imchen, M and Crowley, BL and McGarry, A and Carpenter, L and Bordenstein, SR},
title = {Histone acetylation modulation by a small molecule inhibitor recapitulates symbiont-induced cytoplasmic incompatibility.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116416},
doi = {10.1016/j.celrep.2025.116416},
pmid = {41066235},
issn = {2211-1247},
abstract = {Symbiotic relationships between arthropod hosts and microorganisms have garnered global attention for their influence on host ecology, evolution, and vector control. A major gap in the field is to mechanistically define and reconstitute symbiotic traits in the absence of microbes. Here, we address this omission by identifying an evolutionarily conserved host mechanism that recapitulates Wolbachia-induced cytoplasmic incompatibility (CI)-a paternal-effect embryonic lethality trait. We first show that Wolbachia alter histone acetylation during sperm development in Drosophila melanogaster. By chemically inhibiting histone acetyltransferase (HAT) activity in aposymbiotic males, we reprogram the chromatin landscape of developing sperm to induce a rescuable CI phenotype. This phenotype is further modulated through transgenic knockdown of HAT and histone deacetylase enzymes, providing tunable control over natural CI intensity. Our findings uncover histone acetylation as a key host-intrinsic pathway, capable of inducing symbiont-independent CI for new avenues of basic and applied studies.},
}

@article {pmid41065807,
year = {2025},
author = {Choi, BJ and Kim, JM and Bayburt, H and Choi, DG and Choi, SH and Jeon, CO},
title = {Description of Tateyamaria algicola sp. nov. and Tateyamaria rhodophyticola sp. nov., Isolated from Marine Algae.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {545},
pmid = {41065807},
issn = {1432-0991},
support = {20210469//Ministry of Ocean and Fisheries (KR)/ ; NIBR No. 2024-02-001//National Institute of Biological Resources/ ; 2024//Chung-Ang University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Base Composition ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; Ubiquinone ; Phospholipids/analysis ; Seawater/microbiology ; Sequence Analysis, DNA ; Genome, Bacterial ; },
abstract = {Two aerobic, non-motile, Gram-stain-negative strains, designated SN3-11ᵀ and SN6-1ᵀ, were isolated from marine algae. Both strains were oxidase- and catalase-positive, with rod-shaped morphology. Strain SN3-11ᵀ grew optimally at 25 ℃, pH 7.0-8.0, and 2.0-5.0% (w/v) NaCl, while strain SN6-1ᵀ showed optimal growth at 25 ℃, pH 8.0, and 2.0-3.0% NaCl. Both strains contained ubiquinone-10 as the sole respiratory quinone, and their major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C19:0 cyclo ω8c. Phosphatidylcholine and phosphatidylglycerol were dominant polar lipids, with diphosphatidylglycerol additionally present in SN3-11ᵀ. Strains SN3-11ᵀ and SN6-1ᵀ had genome sizes of 4,762 Kb and 4,157 Kb with G + C contents of 61.3% and 62.0%, respectively. They shared 96.9% 16S rRNA gene sequence similarity, 77.0% average nucleotide identity (ANI), and 20.2% digital DNA-DNA hybridization (dDDH), supporting their classification as distinct species. Their closest relative, Tateyamaria armeniaca KMU-156ᵀ, exhibited 16S rRNA gene sequence similarities of 98.6% to SN3-11ᵀ and 97.7% to SN6-1ᵀ. Phylogenetic trees based on 16S rRNA and whole-genome sequences placed both strains in distinct lineages within Tateyamaria. ANI and dDDH values between the two isolates and other Tateyamaria species were < 78.5% and < 21.0%, respectively. Strains SN3-11ᵀ and SN6-1ᵀ harbored genes encoding diverse carbohydrate-active enzymes and biosynthetic pathways for lycopene, pantothenate, and riboflavin, suggesting potential symbiotic roles with algal hosts. Based on phenotypic, chemotaxonomic, and genomic characteristics, SN3-11ᵀ and SN6-1ᵀ represent two novel species, Tateyamaria algicola sp. nov. (SN3-11ᵀ = KACC 23689ᵀ = JCM 36649ᵀ) and Tateyamaria rhodophyticola sp. nov. (SN6-1ᵀ = KACC 23127ᵀ = JCM 35962ᵀ).},
}

RNA, Ribosomal, 16S/genetics
Phylogeny
Base Composition
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Bacterial Typing Techniques
Nucleic Acid Hybridization
Ubiquinone
Phospholipids/analysis
Seawater/microbiology
Sequence Analysis, DNA
Genome, Bacterial

@article {pmid41065102,
year = {2025},
author = {Pérez-Sepúlveda, M and Jones, AP and Higuita-Aguirre, MI and Holdstock, A and Kafle, A and Cardoso, AA and Vann, R and Mullen, MD and Garcia, K},
title = {Nodulation Is Maintained and Salinity Tolerance Enhanced in Two Soybean Cultivars Inoculated With Sinorhizobium fredii Under Brackish Water.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70570},
doi = {10.1111/ppl.70570},
pmid = {41065102},
issn = {1399-3054},
support = {2020-67013-31800//USDA National Institute of Food and Agriculture/ ; },
mesh = {*Glycine max/microbiology/physiology/drug effects ; *Salt Tolerance/physiology ; *Sinorhizobium fredii/physiology ; Plant Roots/microbiology/physiology/growth & development ; *Plant Root Nodulation/physiology ; Salinity ; Symbiosis ; Plant Shoots/physiology/microbiology ; Biomass ; Potassium/metabolism ; Phosphorus/metabolism ; Nitrogen/metabolism ; },
abstract = {Salinity is an increasing threat to agriculture, particularly in coastal regions affected by seawater intrusion and sea-level rise. This study evaluated the halotolerance and symbiotic potential of Sinorhizobium fredii USDA 208 in two soybean cultivars (includer and excluder) under three salinity levels-low (freshwater), moderate (brackish water), and high (seawater). The results demonstrated that S. fredii not only tolerates but also exhibits enhanced growth under moderate salinity. Nodulation was successfully established when salinity and inoculation occurred simultaneously. Nodulation was also maintained when salinity occurred after the inoculation, particularly in fresh and brackish water. Root development declined with increasing salinity, but the includer cultivar showed better root system architecture plasticity in brackish water, while the excluder cultivar exhibited higher shoot and root biomass across salinity levels. Bacterial inoculation improved shoot phosphorus uptake, the potassium: sodium ratio, and carotenoid retention, particularly in the includer cultivar, suggesting an enhanced physiological tolerance to moderate salinity. Inoculation also resulted in higher shoot nitrogen and maintained pigment content. Using a seawater recipe provides a better understanding of salinity than traditional NaCl-based studies and highlights the role of S. fredii USDA 208 in supporting soybean performance when salts accumulate in coastal agricultural soils.},
}

*Glycine max/microbiology/physiology/drug effects
*Salt Tolerance/physiology
*Sinorhizobium fredii/physiology
Plant Roots/microbiology/physiology/growth & development
*Plant Root Nodulation/physiology
Salinity
Symbiosis
Plant Shoots/physiology/microbiology
Biomass
Potassium/metabolism
Phosphorus/metabolism
Nitrogen/metabolism

@article {pmid41064789,
year = {2025},
author = {Farias, A and Neves, EG and Johnsson, R},
title = {Kuayguara etymatee sp. nov., a New Genus and Species of Artotrogidae (Copepoda: Siphonostomatoida) with an Uncommonly Atrophied Leg 1.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e10},
pmid = {41064789},
issn = {1810-522X},
abstract = {Artotrogidae Brady, 1880 is a cosmopolitan family with 23 valid genera and 131 known species. However, a considerable number of these species were subject of reexaminations and redescriptions recently. With the crescent number of new species discovered, it is becoming possible to better understand their boundaries. This study presents a new genus and species of Artotrogidae, recovered from unidentified hosts in debris of benthonic samples from Todos-os-Santos Bay, northeastern coast of Brazil. Kuayguara etymatee gen. et sp. nov. exhibits an underdeveloped first leg, which possess an unsegmented protopod and 1-segmented exopod, a unique set of morphological characteristics that differentiates it from all other genera of the family.},
}

@article {pmid41064419,
year = {2025},
author = {Corkery, RW and Garvey, CJ and Houston, JE},
title = {In hospite and ex hospite architecture of photosynthetic thylakoid membranes in Symbiodinium spp. using small-angle neutron scattering.},
journal = {Journal of applied crystallography},
volume = {58},
number = {Pt 5},
pages = {1516-1525},
pmid = {41064419},
issn = {0021-8898},
abstract = {We demonstrate that small-angle neutron scattering (SANS) can resolve the architecture of photosynthetic thylakoid membranes in live symbiotic algal cells, both extracted from and living inside their respective hosts (ex hospite and in hospite, respectively). This enables a new non-destructive approach to probing thylakoid organization in coral symbioses, relevant to understanding the mechanisms of coral bleaching. A biologically realistic triple-vesicle model, guided by electron microscopy and established biochemical constraints, was fitted to SANS data from live Symbiodinium associated with both the coral analogue Aiptasia and the reef-building coral Acropora. The resulting compartment scattering length densities, together with established biochemical constraints, define a limited compositional range that supports the plausibility of the structural solution. These fits capture key scattering features and yield dimensional parameters, including inter-thylakoid (IT) gap widths, with uncertainties small enough to test models of stress-related membrane rearrangement. A focused covariance analysis shows that this SANS framework can resolve an IT-gap expansion of ∼2.4 nm with >7σ sensitivity, sufficient to distinguish structural changes proposed in thylakoid stress-response models. This provides a robust baseline for future live-cell studies.},
}

@article {pmid41064255,
year = {2025},
author = {Kong, C and Huang, LB and Yang, MF and Yue, NN and Luo, D and Zhang, Y and Tian, CM and Song, Y and Wei, DR and Shi, RY and Liang, YJ and Yao, J and Wang, LS and Li, DF},
title = {Microbiome engineering: unlocking therapeutic potential in inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610029},
pmid = {41064255},
issn = {1664-302X},
abstract = {The human gut microbiome, traditionally linked to infectious diseases, is now recognized as a hub of non-pathogenic microorganisms that play pivotal roles in host communication and homeostasis. Advances in microbiome engineering have enabled the design of "smart" living therapeutics for inflammatory bowel disease (IBD), leveraging engineered symbiotic bacteria, yeasts, and bacteriophages. This review synthesizes recent progress in reprogramming microbes using synthetic biology tools, emphasizing their capacity to sense pathological signals and deliver targeted therapies. We critically evaluate three key approaches: synthetic gene circuits in bacteria for precision drug delivery, phage-mediated modulation of dysbiotic microbiota, and yeast-based systems for metabolic intervention (e.g., butyrate production). Challenges in biocontainment, genetic stability, and clinical translation are discussed, alongside emerging strategies such as outer membrane vesicles (OMVs) for immunomodulation. By distilling these advances, we highlight a roadmap for translating engineered microbes into safe and effective IBD therapies.},
}

@article {pmid41063423,
year = {2025},
author = {Bartz, PM and Grullón-Penkova, IF and Cavaleri, MA and Reed, SC and Shahid, S and Wood, TE and Bachelot, B},
title = {Experimental warming alters free-living nitrogen fixation in a humid tropical forest.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70592},
pmid = {41063423},
issn = {1469-8137},
support = {1754713//Division of Environmental Biology/ ; 2120085//Division of Environmental Biology/ ; 89243018S-SC-000014//Basic Energy Sciences/ ; 89243018S-SC-000017//Basic Energy Sciences/ ; 89243021S-SC-000076//Basic Energy Sciences/ ; DE-SC-0011806//Basic Energy Sciences/ ; DE-SC-0018942//Basic Energy Sciences/ ; DE-SC0012000//Basic Energy Sciences/ ; DE-SC0022095//Basic Energy Sciences/ ; },
abstract = {Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha[-1] yr[-1]) and by 525% in leaf litter (to 14.518 kg ha[-1] yr[-1]). This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.},
}

@article {pmid41062940,
year = {2025},
author = {Feng, Y and Zou, Z and Liu, C and Zhang, D and Wang, Y and Ma, Y and Cao, Y and Wu, P},
title = {A LjBAK1-associated E3 ubiquitin ligase, LjPUB7, negatively regulates early symbiosis by targeting NFRs.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1334},
pmid = {41062940},
issn = {1471-2229},
support = {24KJB180002//Jiangsu Higher Education Institutions of China/ ; 32090063//The National Science Fundation of China/ ; AMLKF202510//the State Key Laboratory of Agricultural Microbiology/ ; },
mesh = {*Symbiosis/genetics ; *Ubiquitin-Protein Ligases/metabolism/genetics ; Nicotiana/genetics/microbiology/metabolism ; *Plant Proteins/metabolism/genetics ; *Lotus/genetics/enzymology/microbiology/physiology/metabolism ; Ubiquitination ; Gene Expression Regulation, Plant ; },
abstract = {Nod factor receptors (NFRs) are essential for initiating symbiotic signaling in legumes, mediating rhizobial infection and nodule development. Tight regulation of NFR levels is crucial to prevent inappropriate immune responses and maintain cellular homeostasis. Co-expression of LjNFR1 and LjNFR5 triggers cell death in Nicotiana benthamiana, which is specifically inhibited by LjBAK1-mediated ubiquitination and subsequent degradation, suggesting the existence of a LjBAK1-E3 ligase complex for NFR protein turnover. Further analysis identified LjPUB7, a plant U-box E3 ubiquitin ligase in Lotus japonicus, as a regulator of early symbiotic interactions. LjPUB7 interacts with both LjBAK1 and NFRs, and directly ubiquitinates NFRs. Loss-of-function Ljpub7 mutants display increased infection thread formation, enhanced nodule development, and elevated expression of early nodulation genes. These findings reveal that LjPUB7 negatively regulates early rhizobial infection by targeting NFR1 and NFR5 for ubiquitination and degradation, thereby providing insights into the fine-tuned control of symbiotic signaling in legumes.},
}

*Symbiosis/genetics
*Ubiquitin-Protein Ligases/metabolism/genetics
Nicotiana/genetics/microbiology/metabolism
*Plant Proteins/metabolism/genetics
*Lotus/genetics/enzymology/microbiology/physiology/metabolism
Ubiquitination
Gene Expression Regulation, Plant

@article {pmid41061564,
year = {2025},
author = {Marcos-Torres, FJ and Pérez, J and Torrens-González, D and García-Pedrosa, MÁ and Contreras-Moreno, FJ and Moraleda-Muñoz, A},
title = {Global copper response of the soil bacterial predator Myxococcus xanthus and its contribution to antibiotic cross-resistance.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128357},
doi = {10.1016/j.micres.2025.128357},
pmid = {41061564},
issn = {1618-0623},
abstract = {Copper accumulation in agricultural soils poses environmental challenges by selecting copper-resistant bacteria and also contributing to the co-selection of antibiotic-resistant bacteria. In addition, copper influences bacterial predator-prey interactions, potentially altering microbial ecosystems. Myxococcus xanthus, a soil-dwelling bacterium, preys on other microorganisms, including Sinorhizobium meliloti, a symbiotic nitrogen-fixing bacterium associated with leguminous plants. The role of copper in M. xanthus interactions remains poorly understood, although it accumulates at the predator-prey interface. In this study, we explore the transcriptomic response of M. xanthus to copper stress in both monocultures and co-cultures with S. meliloti. Our analysis identified many myxobacterial copper-regulated transcripts, and studies on mutant strains in some copper-induced genes revealed the role of two efflux pumps in cross-resistance to copper and tetracyclines. These findings provide new insights into the adaptive mechanisms of M. xanthus in response to copper, with implications for the co-selection of antibiotic resistance and the broader impact of copper on microbial community dynamics in soil ecosystems.},
}