@article {pmid40405104,
year = {2025},
author = {Lotfy, WA and Ali, AM and Abdou, HM and Ghanem, KM},
title = {Optimization of fermentation conditions for enhanced acetylcholine and biomass production of Lactiplantibacillus plantarum AM2 using the Taguchi approach.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {317},
pmid = {40405104},
issn = {1471-2180},
mesh = {*Fermentation ; *Biomass ; Culture Media/chemistry/metabolism ; *Acetylcholine/biosynthesis/metabolism ; Hydrogen-Ion Concentration ; *Lactobacillus plantarum/metabolism/growth & development ; Glucose/metabolism ; },
abstract = {This study aimed to optimize the fermentation conditions and medium composition for maximum acetylcholine (ACh) and biomass production by Lactiplantibacillus plantarum AM2 using the Taguchi array design, which enables efficient identification of influential variables through minimal experimental runs. Seven key factors were evaluated: beef extract, peptone, yeast extract, glucose, pH, agitation rate, and inoculation size. The optimization process identified the most significant variables influencing ACh and biomass production, with beef extract and peptone being critical for ACh synthesis, while inoculation size was a critical determinant of biomass yield. The optimal conditions for ACh production were determined as beef extract (11 g/l), peptone (40 g/l), yeast extract (5 g/l), glucose (20 g/l), pH 5.7, no agitation, and 1% (v/v) inoculation size, resulting in a predicted ACh concentration of 490.83 pg/ml and an experimental value of 495.8 pg/ml. For biomass production, the optimal conditions were beef extract (8 g/l), peptone (10 g/l), yeast extract (20 g/l), glucose (35 g/l), pH 6.6, agitation at 150 rpm, and 4% (v/v) inoculation size, yielding a predicted biomass of 20.58 g/l and an experimental value of 21.3 g/l. The optimized conditions significantly improved ACh production (6.32-fold) and biomass production (4.56-fold) compared to basal conditions. These findings highlight the efficiency of the Taguchi approach in enhancing the production of ACh and biomass, providing insights into the functional niche of Lactiplantibacillus plantarum AM2 for potential industrial applications and its use in a symbiotic form.},
}

*Fermentation
*Biomass
Culture Media/chemistry/metabolism
*Acetylcholine/biosynthesis/metabolism
Hydrogen-Ion Concentration
*Lactobacillus plantarum/metabolism/growth & development
Glucose/metabolism

@article {pmid40403989,
year = {2025},
author = {Deng, L and Guan, G and Cannon, RD and Mei, L},
title = {Age-related oral microbiota dysbiosis and systemic diseases.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107717},
doi = {10.1016/j.micpath.2025.107717},
pmid = {40403989},
issn = {1096-1208},
abstract = {The oral microbiota is an essential microbial community within the human body, playing a vital role in maintaining health. In older adults, age-related changes in the oral microbiota are linked to both systemic and oral health impairments. The use of various medications for systemic diseases in the elderly can also contribute to the development of oral diseases. Oral microbiota dysbiosis refers to an imbalance in the composition of oral microbial communities. This imbalance, along with disruptions in the host immune response and prolonged inflammation, is closely associated with the onset and progression of several diseases. It contributes to oral conditions such as dental caries, periodontal disease, and halitosis. It is also linked to systemic diseases, including Alzheimer's disease, type 2 diabetes mellitus, rheumatoid arthritis, atherosclerotic cardiovascular disease, and aspiration pneumonia. This review aims to explore how oral microbiota influences specific health outcomes in older individuals, focusing on Alzheimer's disease, type 2 diabetes mellitus, rheumatoid arthritis, atherosclerotic cardiovascular disease, and aspiration pneumonia. The oral microbiota holds promise as a diagnostic tool, therapeutic target, and prognostic biomarker for managing cardiovascular disease, metabolic diseases, infectious diseases and autoimmune diseases. Emphasizing proper oral health care and instilling an understanding of how drugs prescribed for systemic disease impact the oral microbiome, is anticipated to emerge as a key strategy for promoting the general health of older adults.},
}

@article {pmid40402470,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {78},
number = {5},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40402470},
issn = {1472-765X},
mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

*Mycorrhizae/physiology/genetics/classification
New Zealand
*Symbiosis
*Ecosystem
*Plants/microbiology
Soil Microbiology

@article {pmid40401909,
year = {2025},
author = {Morel-Letelier, I and Yuen, B and Orellana, LH and Kück, AC and Camacho-García, YE and Lara, M and Leray, M and Wilkins, LGE},
title = {Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0168624},
doi = {10.1128/msystems.01686-24},
pmid = {40401909},
issn = {2379-5077},
abstract = {Upwelling in the Tropical Eastern Pacific profoundly affects marine coastal ecosystems by driving drastic seasonal changes in water temperature, oxygen levels, and nutrient availability. These conditions serve as a natural experiment that provides a unique opportunity to study how marine animals and their associated microorganisms respond in the face of environmental change. Lucinid bivalves host chemosynthetic Candidatus Thiodiazotropha symbionts equipped with diverse metabolic pathways for sulfur, carbon, and nitrogen use. However, how these symbionts employ their metabolic toolkit in a changing environment remains poorly understood. To address this question, we conducted metagenomic and metatranscriptomic analyses of Ctena cf. galapagana symbionts before and during a Papagayo upwelling event in Santa Elena Bay, Costa Rica. The C. cf. galapagana were co-colonized mainly by two Ca. Thiodiazotropha symbiont clades regardless of the sampling season. We observed a concerted shift in the transcriptomic profiles of both symbiont clades before and during upwelling, suggesting changes in energy source use. Dissimilatory methanol oxidation genes were upregulated before upwelling, while sulfide oxidation genes were upregulated during upwelling. These physiological changes were potentially driven by upwelling-induced changes in sediment biogeochemistry and resource availability. Our findings highlight the adaptability of the lucinid symbiosis and the crucial role of symbiont metabolic flexibility in their resilience to environmental challenges.IMPORTANCEThe oceans are undergoing rapid change, and marine animals together with their associated microorganisms must adjust to these changes. While microbes are known to play a critical role in animal health, we are only beginning to understand how symbiotic relationships help animals cope with environmental variability. Annual upwelling events cause drastic and abrupt increases in nutrient availability and productivity, while temperature and oxygen decrease. In this study, we investigated how bacterial symbionts of the lucinid bivalve Ctena cf. galapagana respond to upwelling in the Tropical Eastern Pacific. The symbionts, from the genus Candidatus Thiodiazotropha, are chemosynthetic (i.e., they use inorganic chemicals for energy and fix carbon) and provide nutrition to their host. Our results show that these symbionts adjust their use of different energy sources in response to environmental changes that affect resource availability. This metabolic flexibility underscores the resilience of animal-microbe relationships in coping with environmental change.},
}

@article {pmid40401050,
year = {2025},
author = {Mager, M and Becker, L and Schulten, N and Fraune, S and Axmann, IM},
title = {Oligonucleotide library assisted sequence mining reveals promoter sequences with distinct temporal expression dynamics for applications in Curvibacter sp. AEP1-3.},
journal = {Synthetic biology (Oxford, England)},
volume = {10},
number = {1},
pages = {ysaf001},
pmid = {40401050},
issn = {2397-7000},
abstract = {The β-proteobacterial species Curvibacter sp. AEP1-3 is a model organism for the study of symbiotic interactions as it is the most abundant colonizer of Hydra vulgaris. Yet, genetic tools for Curvibacter are still in their infancy; few promoters have been characterized so far. Here, we employ an oligonucleotide-based strategy to develop novel expression systems Curvibacter. Potential promoters were systematically mined from the genome in silico. The sequences were cloned as a mixed library into a mCherry reporter vector and positive candidates were selected by Flow Cytometry to be further analysed through plate reader measurements. From 500 candidate sequences, 25 were identified as active promoters of varying expression strength levels. Plate reader measurements revealed unique activity profiles for these sequences across growth phases. The expression levels of these promoters ranged over two orders of magnitudes and showed distinct temporal expression dynamics over the growth phases: while three sequences showed higher expression levels in the exponential phase, we found 12 sequences saturating expression during stationary phase and 10 that showed little discrimination between growth phases. From our library, promoters of the genes dnaK, rpsL and an acyl-homoserine-lactone (AHL) synthase stood out as the most interesting candidates fit for a variety of applications. We identified enriched transcription factor binding motifs among the sorted 33 sequences and genes encoding for homologs of these transcription factors in close proximity to the identified motifs. In this work, we show the value of employing comprehensive high-throughput strategies to establish expression systems for novel model organisms.},
}

@article {pmid40400690,
year = {2025},
author = {Cha, M and Wu, Y and Man, D and Yi, X},
title = {Associations between gut microbiota and diet composition of three arid-adapted rodent species from the Inner Mongolia grassland.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1569592},
pmid = {40400690},
issn = {1664-302X},
abstract = {Food habits are closely associated with the gut microbiota of herbivorous animals; however, limited knowledge exists regarding the arid-adapted rodents. This study investigates the relationship between gut microbiota and dietary composition to offer a scientific basis for comprehending the ecological adaptation strategies of grassland rodents. Cecal contents of Spermophilus alashanicus, S. dauricus, and Meriones unguiculatus were collected and analyzed by using 16S rRNA amplicon sequencing and DNA metabarcoding techniques to determine the structure of gut microbial communities and dietary composition. The results showed that S. alashanicus presented significantly higher gut microbial richness and diversity than S. dauricus and M. unguiculatus. The dominant gut bacterial genera in S. alashanicus and S. dauricus were similar, suggesting that their common genetic backgrounds might influence the colonization and symbiosis of gut microbiota. The three species consumed both plant-based and animal-based foods but differed in their dietary preferences. S. dauricus displayed a significantly higher diversity of animal-based food consumption compared with the other two species. Correlation analysis between diet and gut microbiota indicated that plant-based foods significantly enhanced the diversity and composition of gut microbiota. In contrast, the consumption of animal-based foods significantly decreased microbial diversity. This finding suggests a potential link between the host's genetic background, dietary composition, and the gut microbiota.},
}

@article {pmid40399923,
year = {2025},
author = {Montanari, E and Bernardo, G and Le Noci, V and Anselmi, M and Pupa, SM and Tagliabue, E and Sommariva, M and Sfondrini, L},
title = {Biofilm formation by the host microbiota: a protective shield against immunity and its implication in cancer.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {148},
pmid = {40399923},
issn = {1476-4598},
support = {P2022R5TCA//PRIN, PROGETTI DI RICERCA DI RILEVANTE INTERESSE NAZIONALE/ ; 24718//AIRC IG/ ; },
mesh = {Humans ; *Biofilms/growth & development ; *Neoplasms/immunology/microbiology/etiology/pathology/metabolism ; *Microbiota/immunology ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Human-resident microbes typically cluster into biofilms - structurally organized communities embedded within a matrix of self-produced extracellular polymeric substance (EPS) that serves as a protective shield. These biofilms enhance microbial survival and functional adaptability, favoring a symbiotic relationship with the host under physiological conditions. However, biofilms exhibit a dual role in modulating the immune response. If their ability to promote tolerance is key to safeguarding homeostasis, by contrast, their persistence can overcome the cutting-edge balance resulting in immune evasion, chronic inflammation and development of numerous diseases such as cancer. Recent evidence highlights the significance of cancer-associated microbiota in shaping the tumor microenvironment (TME). These microbial inhabitants often exhibit biofilm-like structures, which may protect them from host immune responses and therapeutic interventions. The presence of biofilm-forming microbiota within the TME may promote chronic inflammation, and release of bioactive molecules that interfere with immune surveillance mechanisms, thereby enabling cancer cells to evade immune destruction. This review delves into the complex interplay between biofilms and cancer, with particular focus on the tumor-associated microbiota and the implications of biofilm involvement in modulating the immune landscape of the TME. Addressing this intricate relationship holds promises for innovative therapeutic approaches aimed at reprogramming the microbiota-cancer axis for better clinical outcomes.},
}

Humans
*Biofilms/growth & development
*Neoplasms/immunology/microbiology/etiology/pathology/metabolism
*Microbiota/immunology
Tumor Microenvironment/immunology
Animals

@article {pmid40399789,
year = {2025},
author = {Mugo, CW and Church, E and Horniblow, RD and Mollan, SP and Botfield, H and Hill, LJ and Sinclair, AJ and Grech, O},
title = {Unravelling the gut-brain connection: a systematic review of migraine and the gut microbiome.},
journal = {The journal of headache and pain},
volume = {26},
number = {1},
pages = {125},
pmid = {40399789},
issn = {1129-2377},
mesh = {Humans ; *Migraine Disorders/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; *Brain-Gut Axis/physiology ; Synbiotics ; },
abstract = {BACKGROUND: There is substantial evidence linking migraines to gastrointestinal (GI) issues. Conditions such as irritable bowel syndrome and colitis often co-occur with migraines and GI symptoms are common among migraine patients. However, the evidence supporting the efficacy of gut microbiome-targeted therapies for managing migraines is limited. This systematic review aimed to describe the existing evidence of the gut microbiome in patients with migraine compared to healthy individuals. Additionally, it sought to examine how therapies targeting the gut microbiome including prebiotics, probiotics and synbiotics, might influence clinical outcomes.

METHODS: We performed searches on Embase, PubMed, and the Cochrane Library to identify studies in migraines and the gut microbiome, focusing on those which investigated the gut microbiome composition and gut microbiome-targeted therapies. Key data was extracted and analysed including study details, patient demographics, migraine type, comorbidities, and clinical outcomes. For gut microbiome composition studies, bacterial diversity and abundance was noted. For gut microbiome-targeted therapies studies, treatment types, dosages, and patient outcomes was recorded.

RESULTS: A significant difference between various genera of microbes was reported between migraine patients and controls in several studies. Bacteroidetes (also named Bacteroidota), proteobacteria, and firmicutes (also named Bacillota) phyla groups were found significantly abundant in migraine, while studies were conflicted in the abundance of Actinobacteria and Clostridia with regards to increased migraine risk in migraine patients. Patients with migraine had a gut microbiome with reduced species number and relative abundance, as well as a distinct bacterial composition compared to controls. Synbiotic and synbiotic/probiotic combination treatments have been shown in five randomised controlled trials and one open label pilot study to significantly decrease migraine severity, frequency, duration and painkiller consumption.

CONCLUSIONS: The significant alterations in microbial phyla observed in migraine patients suggest a potential microbial signature that may be associated with migraine risk or chronic progression. However, the mechanistic underpinnings of these associations remain unclear. This systemic review found that probiotic and synbiotic/probiotic combination therapies may be promising interventions for migraine management, offering significant reductions in migraine frequency and painkiller use. Future randomised controlled studies are needed to evaluate the optimal length of treatment and impact on patient related quality of life.},
}

Humans
*Migraine Disorders/microbiology/therapy
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use
*Brain-Gut Axis/physiology
Synbiotics

@article {pmid40398697,
year = {2025},
author = {Wang, M and Xu, Z and Qiu, J and Dong, B},
title = {Enhanced biogenic manganese oxide production and the removal of Cd(II) and ciprofloxacin via fungus-bacterium co-cultivation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121899},
doi = {10.1016/j.envres.2025.121899},
pmid = {40398697},
issn = {1096-0953},
abstract = {Microbial co-cultivation is a promising strategy for enhancing metabolite production and functional capabilities. While most research on biogenic manganese (Mn) oxidation (BMO) has focused on individual bacterial or fungal strains, the potential benefits of fungal-bacterial co-cultivation remain largely unexplored. In this study, the synergistic effects of co-culturing the Mn-oxidizing fungus Cladosporium sp. XM01 with the Mn-oxidizing bacterium Bacillus sp. XM02 on Mn(II) oxidation were systematically investigated. The results showed that co-cultivation significantly increased total cell biomass and enhanced Mn(II) removal. Optimal conditions were achieved by introducing strain XM02 with a 36 h delay and maintaining a co-culturing ratio of 2:1 (XM01:XM02). The enhanced Mn(II) oxidation observed in the co-culture system was attributed to increased activities of superoxide dismutase and catalase, which help maintain redox homeostasis and sustain the production of superoxide-an essential oxidant in Mn(II) bio-oxidation. Scanning electron microscopy revealed that Bacillus sp. XM02 cells were attached to the hyphae of Cladosporium sp. XM01, forming structured fungal-bacterial aggregates. These aggregates suggest strong physical interactions that likely facilitated nutrient exchange and metabolic cooperation. Additionally, removal kinetics experiments showed that BMO produced in the co-culture exhibited superior Cd(II) adsorption capacity and ciprofloxacin oxidation performance compared to BMO derived from pure cultures. This enhancement was linked to the higher specific surface area and increased average oxidation state (Mn-AOS) of the co-culture BMO, which enhanced its adsorption and oxidative reactivity. These findings provide new insights into the symbiotic interactions among Mn-oxidizing microorganisms and highlight the potential of fungal-bacterial co-cultures as an effective strategy to enhance BMO functionality for environmental remediation.},
}

@article {pmid40398680,
year = {2025},
author = {Zhou, Y and Komnick, MR and Sepulveda, F and Liu, G and Nieves-Ortiz, E and Meador, K and Ndatabaye, O and Fatkhullina, A and Bozicevich, A and Juengel, B and Wu-Woods, NJ and Naydenkov, PM and Kent, J and Christiansen, N and Madariaga, ML and Witkowski, P and Ismagilov, RF and Esterházy, D},
title = {Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.05.003},
pmid = {40398680},
issn = {1935-3456},
abstract = {The REG/Reg gene locus encodes a conserved family of potent antimicrobial but also pancreatitis-associated proteins. Here we investigated whether REG/Reg family members differ in their baseline expression levels and abilities to be regulated in the pancreas and gut upon perturbations. We found, in humans and mice, the pancreas and gut differed in REG/Reg isoform levels and preferences, with the duodenum most resembling the pancreas. Pancreatic acinar cells and intestinal enterocytes were the dominant REG producers. Intestinal symbiotic microbes regulated the expression of the same, select Reg members in gut and pancreas. These Reg members had the most STAT3-binding sites close to the transcription start sites and were partially IL-22 dependent. We thus categorized them as "inducible" and others as "constitutive". Indeed, in pancreatic ductal adenocarcinoma and pancreatitis models, only inducible Reg members were upregulated in the pancreas. While intestinal Reg expression remained unchanged upon pancreatic perturbation, pancreatitis altered the microbial composition of the duodenum and feces shortly after disease onset. Our study reveals differential usage and regulation of REG/Reg isoforms as a mechanism for tissue-specific innate immunity, highlights the intimate connection of pancreas and duodenum, and implies a gut-to-pancreas communication axis resulting in a coordinated Reg response.},
}

@article {pmid40398016,
year = {2025},
author = {Ogo, S and Akama, K and Nakamura, N and Manaka, T and Yamanaka, T},
title = {Symbiosis with Astraeus hygrometricus upregulates cesium and potassium uptake by Pinus densiflora seedlings.},
journal = {Journal of environmental radioactivity},
volume = {287},
number = {},
pages = {107722},
doi = {10.1016/j.jenvrad.2025.107722},
pmid = {40398016},
issn = {1879-1700},
abstract = {After the Fukushima Daiichi Nuclear Power Plant accident in March 2011 in Japan, high activity levels of radiocesium have been reported in wild mushrooms of ectomycorrhizal (EM) fungi. As EM fungal species form symbiotic associations with woody plants, we examined the effect of symbiosis by Astraeus hygrometricus, an EM fungus, on the uptake of cesium (Cs) and potassium (K) by Pinus densiflora seedlings under different levels of K and Cs in the soil in a pot culture. The pine seedlings exhibited enhanced growth due to the symbiosis with A. hygrometricus. The symbiosis with A. hygrometricus significantly increased the Cs and K concentrations of pine seedlings. Cultivating EM seedlings lowered exchangeable K in the soil, although exchangeable Cs did not significantly change. Furthermore, K addition suppresses the Cs absorption of P. densiflora seedlings irrespective of their association with EM fungi.},
}

@article {pmid40397361,
year = {2025},
author = {Lin, YY and Ho, HC and Chou, JY},
title = {Effects of lichen symbiotic bacteria-derived indole-3-acetic acid on the stress responses of an algal-fungal symbiont.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40397361},
issn = {1678-4405},
support = {MOST 111-2621-B-018-001//National Science Council/ ; },
abstract = {Lichens, comprising filamentous fungi and algae/cyanobacteria engaged in mutualistic symbiosis, exhibit remarkable adaptability to environmental challenges. While fungi safeguard algae from dry conditions, their ability to mitigate other stresses remains uncertain. Additionally, the functions of coexisting bacteria within lichen communities remain relatively unexplored. This study investigates the potential of indole-3-acetic acid (IAA) as a stress-response signaling molecule in lichen symbiosis. We subjected IAA-treated monocultures of algae and co-cultures of the fungal-algal complex to various stress conditions. IAA's role in bolstering resilience was evident, as demonstrated by the release of IAA (0-500 µM) by bacteria isolated from the lichen Parmelia tinctorum. This IAA was subsequently utilized by the lichen photobionts to alleviate oxidative stress. IAA acted as a communication signal, priming algal cells to defend against impending stressors. Further microscopic examinations unveiled that only the fibrous extensions were exposed in fungal cells that were in direct physical contact with viable algal cells. Co-cultivation and subsequent microscopic observations revealed that the algal cells were protected from diverse stressors by a barrier of fungal hyphae. Our findings underscore the significance of IAA in enhancing stress resistance within the context of lichen symbiosis, thereby advancing our understanding of the adaptability of these unique organisms. Further exploration of bacterial functions in lichen symbiosis holds promise for uncovering novel insights into their ecology and biology.},
}

@article {pmid40397014,
year = {2025},
author = {Chávez-Jacobo, VM and Reyes-González, AR and Girard, L and Dunn, MF},
title = {The Fsr transporter of Sinorhizobium meliloti contributes to antimicrobial resistance and symbiosis with alfalfa.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
pmid = {40397014},
issn = {1465-2080},
mesh = {*Sinorhizobium meliloti/genetics/drug effects/physiology/metabolism ; *Medicago sativa/microbiology ; *Symbiosis ; Anti-Bacterial Agents/pharmacology/metabolism ; Biofilms/growth & development ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial ; Fosfomycin/pharmacology/analogs & derivatives/metabolism ; *Membrane Transport Proteins/genetics/metabolism ; Plant Roots/microbiology ; },
abstract = {Major facilitator superfamily (MFS) transporters in bacteria participate in both the uptake and export of ions, metabolites or toxic compounds. In rhizobia, specific MFS transporters increase resistance to plant-produced compounds and may also affect other phenotypic traits, including symbiosis with legume host plants. Here, we describe the importance of the Sinorhizobium meliloti 1021 Fsr efflux pump in resistance to selected antimicrobial compounds and in modulating biofilm formation, motility and symbiotic efficiency with alfalfa. The fsr gene (smc00990) is annotated as encoding an MFS family fosmidomycin efflux pump. Unexpectedly, both the 1021 wild type and an fsr null mutant were highly resistant to fosmidomycin. Our assays indicate that this is due to an inability to transport the antibiotic. Unlike the wild type, the fsr mutant was highly sensitive to the fosmidomycin structural analogue fosfomycin, and moderately more sensitive to hydrogen peroxide (H2O2) and deoxycholate (DOC). Root and seed exudates from alfalfa did not inhibit the growth of the wild type or fsr mutant. fsr transcription significantly increased proportionally to the concentration of fosfomycin added to cultures but was unaffected by the addition of other antibiotics, H2O2, DOC or SDS. Alfalfa seed exudate moderately increased fsr transcriptional expression. Fluorometric assays using ethidium bromide as a substrate and carbonyl cyanide m-chlorophenyl hydrazone as an energy decoupler showed that Fsr was a proton-dependent efflux pump. Biofilm formation and swimming motility were decreased and increased, respectively, in the fsr mutant, and its symbiotic efficiency with alfalfa was decreased in terms of nodule numbers per plant and plant dry weights.},
}

*Sinorhizobium meliloti/genetics/drug effects/physiology/metabolism
*Medicago sativa/microbiology
*Symbiosis
Anti-Bacterial Agents/pharmacology/metabolism
Biofilms/growth & development
*Bacterial Proteins/genetics/metabolism
*Drug Resistance, Bacterial
Fosfomycin/pharmacology/analogs & derivatives/metabolism
*Membrane Transport Proteins/genetics/metabolism
Plant Roots/microbiology

@article {pmid40396735,
year = {2025},
author = {Zhang, J and Chen, B-Y and Zhi, M-F and Lin, W-Z and Li, Y-L and Ye, H-L and Xu, S and Zhu, H and Zhou, L-J and Du, L-J and Meng, X-Q and Liu, Y and Feng, Q and Duan, S-Z},
title = {Linking oral microbiota to periodontitis and hypertension unveils that Filifactor alocis aggravates hypertension via infiltration of interferon-γ[+] T cells.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0008425},
doi = {10.1128/msystems.00084-25},
pmid = {40396735},
issn = {2379-5077},
abstract = {UNLABELLED: Periodontal disease (PD), an inflammatory disease initiated by oral microbiota, may aggravate hypertension (HTN). Few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. To investigate the interplay between oral microbiota and hypertension in individuals with periodontitis, we initiated a metagenomic sequencing study on subgingival plaque and saliva samples sourced from HTN patients and those with hypertension and periodontitis (PDHTN). Our primary objective was to characterize species serving as pivotal links (bridge species) in exacerbating hypertension induced by periodontal disease. Within subgingival plaque and saliva specimens, we pinpointed 31 and 28 bridge species, respectively. Furthermore, we noted a decrease in the abundance of nitrate-reducing bacteria, such as Actinomyces spp., Rothia spp., and Veillonella spp., in PDHTN samples. Employing network analysis, we distinguished distinct polymicrobial clusters within the two patient groups. These bridge species coalesced into polymicrobial clusters, revealing intricate symbiotic and competitive relationships. To substantiate our findings, we leveraged an angiotensin II-infused animal model of ligature-induced periodontitis (LIP), confirming the contributory role of Filifactor alocis-a selectively analyzed subgingival bridge species-in exacerbating hypertension and upregulating the frequency of renal CD4[+]IFNγ[+] and CD8[+]IFNγ[+] T cells. Our study screened a list of species linking PD and HTN. PD may aggravate HTN by decreasing the abundance of nitrate-reducing bacteria and increasing the abundance of pathogens. Using an animal model, we demonstrated that F. alocis aggravates HTN via the accumulation of IFNγ[+] T cells in the kidneys.

IMPORTANCE: Both periodontal disease and hypertension are widely prevalent all over the world. PD may aggravate the development of HTN via oral microbiota. However, few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. Here, the present study profiled the oral microbiota in hypertensive participants with periodontitis. We found that the depleted abundance of nitrate-reducing bacteria and the enriched abundance of pathogens. Finally, we validated the role of Filifactor alocis in exacerbating HTN via infiltration of IFNγ[+] T cells in mice kidneys. Our study improved the understanding of oral microbiota linking PD and HTN.},
}

@article {pmid40396656,
year = {2025},
author = {He, J and Van Dingenen, J and Goormachtig, S and Calonne-Salmon, M and Declerck, S},
title = {Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf100},
pmid = {40396656},
issn = {1751-7370},
abstract = {The legume-rhizobia symbiosis possesses great potential for sustainable agriculture because of its ability to fix atmospheric nitrogen, reducing crop dependence on nitrogen fertilizers. Rhizobia recognize the host legume through flavonoids released by the roots. These signals are detected by bacteria typically over a few millimeters. Recent research has shown that arbuscular mycorrhizal fungi extend this recognition beyond 15 cm by transporting flavonoids along their hyphae. In soil, common mycorrhizal networks linking plants are formed by arbuscular mycorrhizal fungi. We hypothesized that such networks linking different legumes can transmit host-specific signals, guiding rhizobia to their appropriate hosts. Using in vitro and greenhouse microcosms, we linked Medicago truncatula and Glycine max via a common mycorrhizal network of Rhizophagus irregularis and inoculated GFP-labeled Sinorhizobium meliloti and mCherry-labeled Bradyrhizobium diazoefficiens on the hyphae. S. meliloti preferentially migrated towards M. truncatula, whereas B. diazoefficiens preferentially migrated towards G. max (155 ± 8 and 13 ± 3 nodules, respectively). This was confirmed in the greenhouse with a higher concentration of S. meliloti (2.1-2.5 × 105 CFU·g-1) near M. truncatula and a higher concentration of B. diazoefficiens (1.5-1.6 × 105 CFU·g-1) near G. max (71-82 and 15-18 nodules, respectively). Metabolomics revealed host-specific flavonoids in hyphal exudates: M. truncatula-connected hyphae released DL-liquiritigenin, naringenin, sakuranetin, and 3,7-dimethylquercetin, whereas G. max-connected hyphae released daidzin, 6"-O-malonyldaidzin, irilone, and erylatissin A. These findings establish that common mycorrhizal networks constitute a "navigation system", using chemical signals to orient rhizobia towards their specific hosts, thereby improving nodulation with potential applications in agriculture.},
}

@article {pmid40395007,
year = {2025},
author = {Castillo-Medina, RE and Islas-Flores, T and Morales-Ruiz, E and Villanueva, M},
title = {Inhibition of protein or glutamine biosynthesis affect the light-induced dephosphorylation of the SBiP1 chaperone in Symbiodiniaceae.},
journal = {Bioscience reports},
volume = {},
number = {},
pages = {},
doi = {10.1042/BSR20241085},
pmid = {40395007},
issn = {1573-4935},
support = {285802//Secretaría de Ciencia Humanidades Tecnología e Innovación (SECIHTI)/ ; },
abstract = {Phosphorylation/dephosphorylation is fundamental for transduction of external stimuli into physiological responses. In photosynthetic dinoflagellates Symbiodinium microadriaticum CassKB8, Thr-phosphorylated SBiP1 under dark conditions, undergoes significant dephosphorylation upon light stimuli. We evaluated the effect of protein synthesis inhibitors on light modulated Thr phosphorylation of SBiP1. Inhibition of cytoplasmic protein synthesis by cycloheximide but not of chloroplastic protein synthesis by chloramphenicol, prevented Thr dephosphorylation of the protein under the light. Additionally, inhibition of glutamine synthetase by glufosinate produced a delay in the light induced dephosphorylation of the chaperone. Heat shock reverted the effect in cycloheximide-treated cells suggesting that heat stress overrides the cycloheximide-induced inhibition of SBiP1 dephosphorylation to hypothetically restore chaperone activity. These results suggest that light and stress are critical switches of SBiP1 chaperone activity that function along with common pathways of protein synthesis and ammonia assimilation, and further confirm that the light induced SBiP1 Thr dephosphorylation is independent of photosynthesis.},
}

@article {pmid40393856,
year = {2025},
author = {Pencik, O and Kolackova, M and Molnarova, K and Huska, D},
title = {What would a hypothetical supercyanobacterium look like?.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.04.006},
pmid = {40393856},
issn = {1879-3096},
abstract = {Over the past two decades, advances in molecular and microbiological methods have broadened the range of microorganisms used in biotechnology. Among them, phototrophic bacteria - especially cyanobacteria - are gaining attention for their potential in tackling climate change and producing biopharmaceuticals. While traditional strains such as Escherichia coli and Bacillus subtilis dominate the field, cyanobacteria offer unique features that present both challenges and opportunities, such as complex gene regulation linked to photosynthesis and carbon fixation, protein sorting, and secretion, as well as the ability to establish novel symbiotic partnerships. This review highlights key developments in engineering cyanobacteria and outlines a vision for a future 'supercyanobacterium' that combines the best traits of current strains, unlocking new possibilities in heterotrophy-dominated biotechnology.},
}

@article {pmid40392778,
year = {2025},
author = {Ballinger, MJ and Perlman, SJ},
title = {Correction: Generality of toxins in defensive symbiosis: Ribosome-inactivating proteins and defense against parasitic wasps in Drosophila.},
journal = {PLoS pathogens},
volume = {21},
number = {5},
pages = {e1013193},
pmid = {40392778},
issn = {1553-7374},
abstract = {[This corrects the article DOI: 10.1371/journal.ppat.1006431.].},
}

@article {pmid40391973,
year = {2025},
author = {Sanath-Kumar, R and Rahman, A and Ren, Z and Reynolds, IP and Augusta, L and Fuqua, C and Weisberg, AJ and Wang, X},
title = {Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion.},
journal = {mBio},
volume = {},
number = {},
pages = {e0104625},
doi = {10.1128/mbio.01046-25},
pmid = {40391973},
issn = {2150-7511},
abstract = {UNLABELLED: Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the C58 lab model, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria and identified two strains distinct from C58 with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed that both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinase XerCD is required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.

IMPORTANCE: Most bacterial genomes are monopartite with a single, circular chromosome. However, some species, like Agrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches, including pathogenesis or symbiosis. Multipartite genomes confer certain advantages; however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage of A. tumefaciens strain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two geographically separated environmental isolates of A. tumefaciens containing fused chromosomes with integration junctions different from the C58 fusion chromosome, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings reveal how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification.},
}

@article {pmid40391904,
year = {2025},
author = {Gasser, MT and Flatau, R and Altamia, MA and Filone, CM and Distel, DL},
title = {Complete genome sequences of two shipworm endosymbiont strains, Teredinibacter turnerae SR01903 and SR02026.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0026525},
doi = {10.1128/mra.00265-25},
pmid = {40391904},
issn = {2576-098X},
abstract = {We present the complete genome sequences of two strains of Teredinibacter turnerae, SR01903 and SR02026, shipworm endosymbionts isolated from the gills of Lyrodus pedicellatus and Teredo bartschi, respectively, and derived from Oxford Nanopore sequencing. These sequences will aid in the comparative genomics of shipworm endosymbionts and symbiosis model development.},
}

@article {pmid40391446,
year = {2025},
author = {Otjacques, E and Jatico, B and Marques, TA and Xavier, JC and Ruby, E and McFall-Ngai, M and Rosa, R},
title = {Climate-Driven Warming Disrupts the Symbiosis of Bobtail Squid Euprymna scolopes and the Luminous Bacterium Vibrio fischeri.},
journal = {Global change biology},
volume = {31},
number = {5},
pages = {e70243},
doi = {10.1111/gcb.70243},
pmid = {40391446},
issn = {1365-2486},
support = {LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; UI/BD/151019/2021//Fundação para a Ciência e a Tecnologia/ ; UIDB/00006/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04292/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Aliivibrio fischeri/physiology ; *Decapodiformes/microbiology/physiology ; *Symbiosis ; *Climate Change ; Temperature ; },
abstract = {Under the current climate crisis, marine heatwaves (MHW) are expected to intensify and become more frequent in the future, leading to adverse effects on marine life. Here, we aimed to investigate the impact of environmental warming on the symbiotic relationship between the Hawaiian bobtail squid (Euprymna scolopes) and the bioluminescent bacterium Vibrio fischeri. We exposed eggs of E. scolopes to three different temperatures during embryogenesis, namely: (i) 25°C (yearly average), (ii) 27°C (summer maximum) or (iii) 30°C (category IV MHW), followed by a colonisation assay under the same conditions. Decreased hatching success and reduced developmental time were observed across warmer conditions compared to 25°C. Moreover, exposure to the category IV MHW led to a significant decrease in survival after 48 h. With increasing temperature, bobtail squids required more bacteria in the surrounding seawater for successful colonisation. When colonised, the regression of the light organ's appendages was not dependent on temperature, but the opposite was found in non-colonised bobtail squids. Furthermore, the capacity for crypt 3 formation in the squid's light organ, which is crucial for enhancing resilience under stress, also declined with warming conditions. This study emphasises the critical need to study the dynamics of microbial symbiosis under the projected conditions for the ocean of tomorrow.},
}

Animals
*Aliivibrio fischeri/physiology
*Decapodiformes/microbiology/physiology
*Symbiosis
*Climate Change
Temperature

@article {pmid40390499,
year = {2025},
author = {Patel, P and Patel, F and Joshi, C and Joshi, M},
title = {Whole genome analysis of endophytic strain PM1 reveals promising plant Growth-Promoting mechanisms in pomegranate.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {2},
pages = {100486},
pmid = {40390499},
issn = {2090-5920},
abstract = {The plant ecosystem harbours diverse symbiotic microorganisms with plant growth promoting and biocontrol activities. The gram- negative endophytic bacterium PM1 strain, isolated from the nodal region of pomegranate. The strain PM1 was studied through whole-genome sequencing, functional annotation, and plant growth-promoting trait (PGPT) gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Brucella. The assembled genome size was 5,200,895 bp with a G + C content of 56.4 %. The average nucleotide identity (ANI) analysis revealed a 97.62 % similarity between PM1 and B. anthropi ATCC 49188 T, a type strain derived from human clinical samples, indicating a close relationship with Brucella anthropi. The functional annotation revealed 2,945 PGPT-related genes, including 32 % linked to direct effects (phytohormone signal production, biofertilization, and bioremediation processes) and 67 % to indirect effects (plant colonization, biocontrol, and competitive exclusion). KEGG analysis revealed genes involved in nitrogen metabolism, phosphate solubilization, siderophore production, hormone biosynthesis (gibberellin, cytokinin, and auxin), root colonization, and stress mitigation. Virulence factor database (VFDB) data revealed the absence of complete virulence gene assemblies, indicating limited pathogenic potential. Furthermore, secondary metabolite analysis predicted the potential production of ochrobactin compounds, which are potent siderophores that are important traits associated with PGPTs. The complete genome analysis of Brucella sp. PM1 provides new insights into plant-bacteria interactions, laying a foundation for advanced postgenomic studies and facilitating the development of bioeffective strategies such as biofertilizers or biocontrol agents for sustainable improvement in crop yields.},
}

@article {pmid40388617,
year = {2025},
author = {Paries, M and Hobecker, K and Hernandez Luelmo, S and Binci, F and Guercio, A and Usländer, A and Cardoso, C and Si, Y and Wankner, L and Bashyal, S and Troycke, P and Brückner, F and Pimprikar, P and Shabek, N and Gutjahr, C},
title = {The GRAS protein RAM1 interacts with WRI transcription factors to regulate plant genes required for arbuscule development and function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2427021122},
doi = {10.1073/pnas.2427021122},
pmid = {40388617},
issn = {1091-6490},
support = {170483403 SFB924_TP B03//Deutsche Forschungsgemeinschaft (DFG)/ ; 759731//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; XX//Alexander von Humboldt Foundation/ ; 2047396//NSF (NSF)/ ; 2139805//NSF (NSF)/ ; XX//Max-Planck-Society/ ; },
mesh = {*Gene Expression Regulation, Plant ; *Transcription Factors/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; *Mycorrhizae/genetics/physiology/growth & development/metabolism ; Symbiosis/genetics ; Promoter Regions, Genetic ; Plant Roots/microbiology/genetics/metabolism ; Nicotiana/genetics ; *Arabidopsis Proteins/metabolism/genetics ; Arabidopsis/genetics/metabolism ; },
abstract = {During arbuscular mycorrhiza (AM) symbiosis AM fungi form tree-shaped structures called arbuscules in root cortex cells of host plants. Arbuscules and their host cells are central for reciprocal nutrient exchange between the symbionts. REQUIRED FOR ARBUSCULAR MYCORRHIZATION1 (RAM1) encodes a GRAS protein crucial for transcriptionally regulating plant genes needed for arbuscule development and nutrient exchange. Similar to other GRAS proteins, RAM1 likely does not bind to DNA and how RAM1 activates its target promoters remained elusive. Here, we demonstrate that RAM1 interacts with five AM-induced APETALA 2 (AP2) transcription factors of the WRINKLED1-like family called CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), WRI3, WRI5a, WRI5b, and WRI5c via a C-terminal domain containing the M2/M2a motif. This motif is conserved and enriched in WRI proteins encoded by genomes of AM-competent plants. RAM1 together with any of these WRI proteins activates the promoters of genes required for symbiotic nutrient exchange, namely RAM2, STUNTED ARBUSCULES (STR), and PHOSPHATE TRANSPORTER 4 (PT4), in Nicotiana benthamiana leaves. This activation as well as target promoter induction in Lotus japonicus hairy roots depends on MYCS (MYCORRHIZA SEQUENCE)-elements and AW-boxes, previously identified as WRI-binding sites. The WRI genes are activated in two waves: Transcription of RAM1, CBX1, and WRI3 is coregulated by calcium- and calmodulin-dependent protein kinase-activated CYCLOPS, through the AMCYC-RE in their promoter, and DELLA, while WRI5a, b, and c promoters contain MYCS-elements and AW-boxes and can be activated by RAM1 heterocomplexes with CBX1 or WRI3. We propose that RAM1 provides an activation domain to DNA-binding WRI proteins to activate genes with central roles in AM development and function.},
}

*Gene Expression Regulation, Plant
*Transcription Factors/metabolism/genetics
*Plant Proteins/metabolism/genetics
*Mycorrhizae/genetics/physiology/growth & development/metabolism
Symbiosis/genetics
Promoter Regions, Genetic
Plant Roots/microbiology/genetics/metabolism
Nicotiana/genetics
*Arabidopsis Proteins/metabolism/genetics
Arabidopsis/genetics/metabolism

@article {pmid40387630,
year = {2025},
author = {Yee, DP and Juery, C and Toullec, G and Catacora-Grundy, A and Lekieffre, C and Wangpraseurt, D and Decelle, J},
title = {Physiology and metabolism of eukaryotic microalgae involved in aquatic photosymbioses.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70190},
pmid = {40387630},
issn = {1469-8137},
support = {GBMF11532//Gordon and Betty Moore Foundation/ ; 101088661//H2020 European Research Council - Consolidator/ ; (GA#101059915)//H2020 European Union BiOcean5D/ ; },
abstract = {Symbiosis between eukaryotic microalgae and heterotrophic hosts is a widespread, phylogenetically convergent, and ecologically important phenomenon in aquatic ecosystems. Partners include taxonomically diverse microalgae interacting with multicellular or unicellular hosts in marine or freshwater environments. While progress has been made recently, there are still major knowledge gaps on the microenvironmental conditions of microalgae in hospite (e.g. nutrient and CO2 availability), the algal carbon metabolism (production and storage), and the cellular mechanisms of carbohydrate export to the host. This review aims to provide current knowledge on the physiology and metabolism of symbiotic microalgae, to highlight whether there are commonalities across different photosymbioses, and to identify new approaches and technologies for disentangling photosymbiotic interactions at relevant temporal and spatial scales.},
}

@article {pmid40387602,
year = {2025},
author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J},
title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e70013},
pmid = {40387602},
issn = {1550-7408},
support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovación y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation & purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; },
abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.},
}

Animals
Phylogeny
*Sea Cucumbers/parasitology
*Apicomplexa/genetics/classification/isolation & purification
Host Specificity
Female
Host-Parasite Interactions
Genome, Mitochondrial

@article {pmid40386899,
year = {2025},
author = {Pa, M and Iyer, K and Koul, V and Kochar, M},
title = {Regulatory Players in Mycorrhizal-Bacterial-Plant Interactions.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70053},
doi = {10.1002/jobm.70053},
pmid = {40386899},
issn = {1521-4028},
support = {//The financial support of Council of Scientific and Industrial Research (CSIR), Govt. of India (Grant No. 38(1521)/21/EMR-II) and Director General, TERI, for providing the required infrastructure and facilities to carry out our research work./ ; },
abstract = {Mycorrhizae contribute significantly for plant growth and development, often providing nutrients such as phosphate and nitrogen, while also enhancing stress tolerance and resistance against phytopathogens. Plant symbiotic mycorrhizal networks harbor bacterial communities that aid mycorrhizal functions and augment plant nutrition and development. Various bacterial associations of mycorrhiza bring forth advantageous traits to mycorrhizal symbiosis and host colonization, which involves a wide range of signaling and regulatory molecules. These regulatory molecules play an important role in adapting and responding to new microenvironments with different hosts through the production of metabolites and expression of favorable genes. Small molecular components such as noncoding RNA (miRNA and sRNA) are also involved in the regulation and adaptation to these microenvironments. Regulatory pathways involving protein kinases play an important role in the tripartite association of bacteria and mycorrhizal fungi with plants, and the subsequent promotion of symbiotic interactions. This mini-review highlights potential bacterial regulatory candidates which can influence mycorrhiza-plant interactions to significantly benefit plant growth and development. An understanding of these bacterial regulatory mechanisms may suggest new strategies for knowledge-based application in crop productivity improvement programs.},
}

@article {pmid40385569,
year = {2025},
author = {Fernández-Vargas, R and Jiménez-Alpízar, S and Leandro-Arce, V and Mendoza-Guido, B and Rojas-Jimenez, K},
title = {Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests.},
journal = {Access microbiology},
volume = {7},
number = {5},
pages = {},
pmid = {40385569},
issn = {2516-8290},
abstract = {Here, we report the draft genome sequences of four Bradyrhizobium spp. isolates obtained from root nodules of the native legumes Pentaclethra macroloba, Chamaecrista nictitans, Erythrina fusca and Zygia engelsingii in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed that these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared with their closest Bradyrhizobium species. Functional annotation revealed some genes related to nitrogen fixation (nifA, nifB, nifH) and nodulation capacity (nodB, nodC, nodJ). These results provide insights into the diversity and symbiotic capabilities of Bradyrhizobium in tropical ecosystems.},
}

@article {pmid40385373,
year = {2025},
author = {Rodak, NY and Tan, CH and Sternberg, PW},
title = {A small-scale bacterial-based liquid Culture Method for Steinernema hermaphroditum.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40385373},
issn = {2578-9430},
abstract = {Entomopathogenic nematodes (EPN) infect and kill their insect host with the help of symbiotic bacteria. The only known hermaphroditic (androdiecious) EPN, the clade IV Steinernema hermaphroditum , offers opportunities for exploring both parasitic and mutualistic symbiosis, as well as for evolutionary and developmental studies. Experimental and genetic analysis of this animal is now facilitated through the development of forward and reverse genetic tools and improved culturing techniques. Here, we describe a liquid-culture technique adapted for this worm. The method can be a starting point for the development of large-scale cultivation of the worm and provides a method to generate infective juveniles without an insect host and either with or without its native symbiotic bacteria.},
}

@article {pmid40385307,
year = {2025},
author = {McLaren, GC and Farrell, MV and Shikuma, NJ and Tran, C},
title = {Photosynthetic dependence and filament production in physical bacterial-Symbiodiniaceae interactions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf070},
pmid = {40385307},
issn = {2730-6151},
abstract = {The cnidarian microbiome consists of a wide variety of beneficial microbes that play vital roles in maintaining and fortifying host health. Photosynthesis from symbiotic dinoflagellates (in the family Symbiodiniaceae) is crucial for their symbiosis establishment with the cnidarian host. Although more is known regarding interactions between the host and its associated bacteria and dinoflagellates, there has been little investigation into the relationship between the two microbes themselves and whether photosynthesis plays a role. Through two different methods of photosynthetic inhibition of dinoflagellates (incubation in the dark or pre-treatment with a photosystem II inhibitor), we investigated how pathogenic versus beneficial bacteria physically interact with three Symbiodiniaceae strains (symbiotic and free-living). The beneficial bacterium Tritonibacter mobilis appears to interact with photosynthesizing algae only. In the absence of photosynthesis, little to no physical interactions were observed between Symbiodiniaceae and T. mobilis. Bacterial congregation around individual dinoflagellate cells was significantly lower when photosynthesis was impaired, suggesting photosynthesis is a key facilitator of interactions between T. mobilis and all three Symbiodiniaceae strains. We also investigated whether photosynthesis affects interactions between Symbiodiniaceae and the pathogen Vibrio alginolyticus. Although no discernable impacts of photosynthetic inhibition were observed with the pathogen, scanning electron microscopy uncovered various mechanisms of interaction between Symbiodiniaceae and both bacteria, one of which includes the production of filaments not previously described. Overall, our research highlights the importance of photosynthesis in initiating interactions between bacteria and both free-living and symbiotic dinoflagellates, and opens a door to new questions regarding cell-surface interactions among individual microbes.},
}

@article {pmid40385219,
year = {2025},
author = {Halder, U and Radharamanan, C and Venkatesan, K and Perumal, S},
title = {Inhibition of Peanut (Arachis hypogaea L.) Growth, Development, and Promotion of Root Nodulation Including Plant Nitrogen Uptake Triggered by Polyvinyl Chloride Microplastics.},
journal = {ACS omega},
volume = {10},
number = {18},
pages = {18668-18681},
pmid = {40385219},
issn = {2470-1343},
abstract = {Agroecosystem sustainability and global food security may be threatened by the widespread presence and distribution of microplastics (MPs). This study investigates the impact of polyvinyl chloride (PVC) microplastics with four different dosages (0.5, 1.5, 2.5, and 3.5%) on the growth, development, and nitrogen uptake of peanut (Arachis hypogaea L.), a legume that forms symbiotic relationships with nitrogen-fixing root nodules. Oxidative stress was indicated by increases in the activity of hydrogen peroxide, proline, superoxide dismutase, peroxidase, and ascorbate peroxidase of 54.3, 72.93, 135.74, 41.59, and 44.59%, respectively, for the 3.5% dose (T4) and malondialdehyde and catalase of 23.7 and 17.52%, respectively, for the 2.5% dose (T3) over the control. Peanut seedlings' growth and development were inhibited through the suppression of chlorophyll a (30.92%), chlorophyll b (36.36%), and carotenoid (25.65%) for treatment 2 (T2) and plant height (19.52% for T4), plant dry weight (46.09%), leaf number (18.86%), and branch length (59.37%) for T4. However, root nodule number, weight, and plant N content promoted 30.19-72.32, 55.88-141.16, and 1.46-7.01%, respectively, from control to T4, which may be an adaptive mechanism for legumes to overcome N deficiency through the morphological and physiological adjustments in the stressed conditions. The study outcomes may provide worthy implications for correctly managing peanut crops in PVC MP-contaminated soil, which will ensure food security and ecosystem sustainability.},
}

@article {pmid40384928,
year = {2025},
author = {Songwattana, P and Boonchuen, P and Pruksametanan, N and Teamtisong, K and Sato, S and Hashimoto, S and Higashitani, N and Kawaharada, Y and Araragi, M and Okazaki, S and Piromyou, P and Wongdee, J and Greetatorn, T and Giraud, E and Boonkerd, N and Tittabutr, P and Teaumroong, N},
title = {Elucidation of the symbiotic incompatibility mechanisms between Vigna radiata and Bradyrhizobium vignae ORS3257 mediated by nodulation outer protein P2.},
journal = {iScience},
volume = {28},
number = {5},
pages = {112351},
pmid = {40384928},
issn = {2589-0042},
abstract = {Bradyrhizobium vignae ORS3257 is an efficient symbiotic strain for Vigna unguiculata and V. mungo but fails with V. radiata due to an effector-triggered immunity response mediated by the nodulation outer protein P2 (NopP2). To understand this incompatibility, we identified NopP2 interacting proteins in V. radiata cv. KPS1, including enolase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), monodehydroascorbate reductase (MDHAR), and serine hydroxymethyltransferase (SHMT) as targets. Protein-protein interaction assays confirmed that NopP2 binds to these enzymes, and further analysis revealed their co-localization on the plasma membrane. Comparative transcriptomic analysis revealed NopP2 stimulates genes related to plant defense response (PR1, PR5, MYB13, and TAO1), hydrogen peroxide (SOD, POX10, and POX16), and cell wall lignification (LAC). NopP2 did not alter the expression of genes encoding the target enzymes but interfered with MDHAR activity, leading to high H2O2 accumulation in roots. These findings suggest that NopP2 contributes to symbiotic incompatibility in V. radiata by inducing a multifaceted defense response and initiating cell wall lignification early in infection.},
}

@article {pmid40384784,
year = {2025},
author = {DiSalvo, S and Maness, N and Braun, A and Tran, M and Hofferkamp, A},
title = {Tracking tripartite interaction dynamics: isolation, integration, and influence of bacteriophages in the Paraburkholderia-Dictyostelium discoideum symbiosis system.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537073},
pmid = {40384784},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacteriophages influence interactions between bacterial symbionts and their hosts by exerting parasitic pressure on symbiont populations and facilitating bacterial evolution through selection, gene exchange, and prophage integration. Host organisms also modulate phage-bacteria interactions, with host-specific contexts potentially limiting or promoting phage access to bacterial symbionts or driving alternative phenotypic or evolutionary outcomes.

METHODS: To better elucidate tripartite phage-bacteria-host interactions in real-time, we expanded the Dictyostelium discoideum-Paraburkholderia symbiosis system to include Paraburkholderia-specific phages. We isolated six environmental Paraburkholderia phages from soil samples using a multi-host enrichment approach. We also identified a functional prophage from monocultures of one of the Paraburkholderia symbiont strains implemented in the enrichment approach. These phages were evaluated across all three amoeba-associated Paraburkholderia symbiont species. Finally, we treated Paraburkholderia infected amoeba lines with select phage isolates and assessed their effects on symbiont prevalence and host fitness.

RESULTS: The isolated phages exhibited diverse plaquing characteristics and virion morphologies, collectively targeting Paraburkholderia strains belonging to each of the amoeba-symbiotic species. Following amoeba treatment experiments, we observed that phage application in some cases reduced symbiont infection prevalence and alleviated host fitness impacts, while in others, no significant effects were noted. Notably, phages were able to persist within the symbiont-infected amoeba populations over multiple culture transfers, indicating potential long-term interactions.

DISCUSSION: These findings highlight the variability of phage-symbiont interactions within a host environment and underscore the complex nature of phage treatment outcomes. The observed variability lays the foundation for future studies exploring the long-term dynamics of tripartite systems, suggesting potential mechanisms that may shape differential phage treatment outcomes and presenting valuable avenues for future investigation.},
}

@article {pmid40384569,
year = {2025},
author = {Kwon, EH and Adhikari, A and Khan, AL and Do, E and Methela, NJ and Lee, CY and Kang, SM and Ku, KM and Yun, BW and Lee, IJ},
title = {Microbial Melatonin Production Improves Plant Metabolic Function in Short-Term Climate-Induced Stresses.},
journal = {Journal of pineal research},
volume = {77},
number = {3},
pages = {e70052},
pmid = {40384569},
issn = {1600-079X},
mesh = {*Melatonin/biosynthesis ; *Glycine max/metabolism/microbiology ; *Bacillus/metabolism ; *Stress, Physiological ; *Climate Change ; },
abstract = {Climate change, specifically high temperatures, can reduce soil moisture and cause hypersaline conditions, which creates an unsustainable agro-production system. Microbial symbionts associated with plants relinquish stressful conditions by producing stress-protecting substances. Melatonin is a signaling and stress-protecting molecule for plants, but is least known for microbial symbionts and their function in stress protection. Here, our study shows that the melatonin-synthesizing Bacillus velezensis EH151 (27.9 ng/mL at 96 h) significantly improved host plant (Glycine max L.) growth, biomass, photosynthesis, and reduced oxidative stress during heat and salinity stress conditions than the non-inculcated control. The EH151 symbiosis enhanced the macronutrient (P, Ca, and K) and reduced Na uptake in shoots during stress conditions. The microbial inoculation significantly expressed the high-affinity K[+] transporter, MYB transcription factor, Salt Overly Sensitive 1, Na[+]/H[+] antiporter 2, and heat shock transcription factors in spatio-temporal orders during heat and salinity stress (H&S 1, 3, 10, and 14 h). We observed that microbial strain significantly increased the plant's endogenous abscisic acid (49.5% in H&S 10 h), jasmonic acid (71% in H&S 10 h), and melatonin biosynthesis (418% in H&S 14 h). Metabolome map of plant defense response showed that EH151 enhanced activation of amino acid metabolism pathways (e.g., glutamate (34%) L-aspartate (82%), glycine (18.5%), and serine (58%) under H&S 14 h compared to non-inoculation). Conversely, the free sugars and organic acids within the central carbon metabolism were significantly activated in non-inoculated combined heat and salinity stress compared to inoculated plants-suggesting lesser defense energy activated for stress tolerance. In conclusion, the current results show promising effects of the microbial abilities of melatonin that can regulate host growth and defense responses. Utilization of beneficial strains like B. velezensis EH151 could be the ideal strategy to improve stress tolerance and overcome the adverse impact of climate-induced abrupt changes.},
}

*Melatonin/biosynthesis
*Glycine max/metabolism/microbiology
*Bacillus/metabolism
*Stress, Physiological
*Climate Change

@article {pmid40383418,
year = {2025},
author = {Dellagnola, FA and Yunes, AN and Vega, IA},
title = {Unravelling the Consortium of the Cercarial Dermatitis in Lake from a Basin of Argentinian Central Andes: Histological and Phylogenetic Insights of Chilina Snail and their Fluke Partner.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107650},
doi = {10.1016/j.actatropica.2025.107650},
pmid = {40383418},
issn = {1873-6254},
abstract = {In the context of a research program dealing with the symbiotic associations between aquatic snails and trematodes, we studied a host-parasite consortium in Lake El Nihuil (Mendoza, Argentina), a water body from Atuel river basin (Central Andes) in which recent outbreaks of cercarial dermatitis ('swimmer's itch') occurred. According to the morphological traits and molecular phylogenetic analyses (mitochondrial COI and 16S rRNA genes), the gastropod host was assigned to the endemic genus Chilina. The snails hosted and released a schistosomatid brevifurcate apharingeate cercaria, whose phylogenetic position was inferred using 28S rRNA subunit gene and 18S-ITS1-5.8S rRNA ribosomal region. The parasite was placed in a clade together with sequences from 'Furcocercariae Lineage II', avian schistosomes closely related to the recently named genus Nasusbilharzia, whose final host, the endemic black-necked swan, occurs in Lake El Nihuil. The infected specimens of Chilina sp. showed abundant parasite larvae placed between haemocoelic spaces and connective tissues, modifying the histological architecture of the digestive gland-gonad complex. Parasites produced a decrease in the number of glandular acini and atrophy of the reproductive tissue. This work suggests a displacement of the swimmer's itch outbreaks towards lower latitudes, highlighting the need for the implementation of multidisciplinary studies to monitor these emerging diseases in association with specific symbiotic consortiums.},
}

@article {pmid40383409,
year = {2025},
author = {Hu, D and Zhao, J and Wu, M and Zhou, Y and Lyu, B and Xu, C and Huang, C and Su, Z and Zhang, H and Guo, J and Tang, W and Chen, G and Li, Q},
title = {Microbial Interactions Induce the Mutational Signature of Mismatch Repair Deficiency in Colorectal Cancer and Associated with EPPK1 Mutations.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217807},
doi = {10.1016/j.canlet.2025.217807},
pmid = {40383409},
issn = {1872-7980},
abstract = {To better understand the impact of microbial interactions on the clonal evolution of colorectal cancer (CRC), we conducted high-resolution profiling of the gut microbiome of 101 treatment-naïve primary CRC patients using nanopore sequencing. We performed an integrated analysis of microbiome and tumor exome data to identify symbiotic microbes that interactively influence the mutational processes and the subsequent clonality of CRC. Our results suggested that Dialister pneumosintes and Fusobacterium animalis were both associated with somatic EPPK1 mutations and promote SBS6 (mismatch repair deficiency, dMMR) activity. Notably, we showed that the symbiotic architecture of Dialister pneumosintes and Fusobacterium animalis undergoes significant changes with the mutational status of EPPK1. In addition, we identified specific metabolic pathways involving key metabolites that potentially mediate microbial interactions in CRC. These findings provide new insights into the interplay between the gut microbiome and the mutation landscape of colorectal cancer, thereby informing the clonal evolution of CRC and new strategies for precision medicine.},
}

@article {pmid40383313,
year = {2025},
author = {Ren, J and Ren, X and Deng, Z and Zhang, H and Wang, J and Zhang, C and Lu, F and Shi, J},
title = {Ecological effects of biochar in heavy metal-contaminated soils from multidimensional perspective: Using meta-analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132695},
doi = {10.1016/j.biortech.2025.132695},
pmid = {40383313},
issn = {1873-2976},
abstract = {The application of biochar in the remediation of heavy metal-contaminated soil shows great potential, but its comprehensive impacts on metal dynamics and the soil ecosystem have not been quantified. This study conducted a meta - analysis of 496 observations from 41 studies. The results indicated that biochar can significantly decrease the bioavailability of cationic metals, but has limited effect on anionic heavy metals. After application, soil nutrient content and enzyme activity significantly increased. Microbial network analysis revealed enhanced interactions between species, and the reconstruction of the core microbial community indicated a shift in microbial survival strategies from resisting heavy metal stress to nutrient cycling and plant symbiosis. FAPROTAX analysis showed that microbial communities related to nitrogen and sulfur cycles were significantly stimulated. This study explores the role of biochar in restoring soil multifunctionality while addressing metal pollution issues from multiple perspectives, offering key insights for developing targeted soil remediation strategies.},
}

@article {pmid40382964,
year = {2025},
author = {Wang, X and Ni, R and Li, L and Yu, H and Qi, J and Ma, B and Hu, C and Qu, J},
title = {Algae-driven bacterial production of extracellular reactive oxygen species for emerging contaminants degradation.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179670},
doi = {10.1016/j.scitotenv.2025.179670},
pmid = {40382964},
issn = {1879-1026},
abstract = {Emerging contaminants (ECs) are ubiquitous in natural surface waters, posing significant risks to aquatic ecosystems and human health. Symbiotic systems comprising photoautotrophic algae and associated bacteria offer a promising approach for the bioremediation of aquatic environments. This study investigated the degradation of five ECs (carbamazepine, diclofenac, atenolol, sulfamethoxazole, and ofloxacin) by reactive oxygen species (ROS) generated through algal-bacterial interactions. The algal-bacterial system exhibited superior degradation efficiencies, achieving 96 %, 97 %, 89 %, 72 %, and 77 % removal for the respective ECs after 6 days, far surpassing the performance of pure bacterial or algal systems. Elevated levels of biogenic ROS were observed in the algal-bacterial system, with extracellular superoxide radicals (O2[•-]) and hydrogen peroxide (H2O2) identified as key drivers of the degradation process. Under ECs stress, the algal-bacterial system maintained cellular integrity and metabolic activity by upregulating pathways related to carbohydrate, lipid, amino acid, and nucleotide metabolism, thereby enhancing its resistance. These findings highlight the significant potential of algal-bacterial systems for the transformation of ECs, offering a sustainable strategy for bioremediation and the restoration of ecosystem health.},
}

@article {pmid40382931,
year = {2025},
author = {Subedi, SC and Epps, S and Ankrah, N and Bhandari, S},
title = {Soil microbes' role in plant germination and growth under salt stress.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125841},
doi = {10.1016/j.jenvman.2025.125841},
pmid = {40382931},
issn = {1095-8630},
abstract = {One significant consequence of climate change is the rising sea levels, which contribute to the intrusion of saltwater towards the inland and groundwater placing extreme salt stress on many plants. Beneficial interactions with microorganisms may be crucial for ameliorating salt stress and facilitating the ecosystem services plants provide. We aimed to test if microbes aid plants in coping with salinity stress and to identify potential applications for enhancing plant resilience in the face of ongoing environmental changes. We set up a factorial experiment that manipulated the introduction of field collected soil microbes, the salinity of these introduced microbes, and the salinity of the water in which plants were grown (freshwater vs. saltwater). To identify the impact of native microbes on the survival of plants in high stress environments, specifically we examined how a Liatris spicata, a freshwater plant would germinate and grow in salt environments. The overall germination of L. spicata showed that native microbes from high salinity sites positively affect the growth of plants in saltwater. Germination rate was significantly higher (25.8 %) in plants with microbes compared to control plants. Both saltwater exposure and microbial presence had a significant effect on plant growth, suggesting that the impact of saltwater on plant growth depends on the presence of microbes. Our results revealed a significant decrease in the number of microbial colony-forming units (CFUs) in response to saltwater treatment (p < 0.001). Both fungal and bacterial CFUs were significantly reduced in saltwater-treated soils compared to freshwater soils. These findings highlight the potential role of native soil microbes in enhancing plant resilience to salinity stress, offering valuable insights for improving plant survival and productivity in increasingly saline environments.},
}

@article {pmid40382556,
year = {2025},
author = {Zhang, X and Yang, L and Cai, T and Liao, H and Cai, P and Zhao, X and Gu, N and Yue, Z and Gu, Y and Zhang, F and Wu, C and Lu, X},
title = {The natural symbiotic bacterium Enterococcus faecalis LX10 drives Bombyx mori refractoriness to Nosema bombycis infection via the secretion of enterococcin.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {303},
pmid = {40382556},
issn = {1471-2180},
support = {Y20235377//A Project Supported by Scientific Research Fund of Zhejiang Provincial Education Department/ ; 2024YZ07//The General Plan Project of Huzhou Science and Technology Bureau/ ; },
mesh = {Animals ; *Enterococcus faecalis/metabolism/physiology/genetics ; *Bombyx/microbiology/immunology ; *Symbiosis ; *Nosema/physiology/pathogenicity ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {BACKGROUND: The microsporidian Nosema bombycis is an obligate intracellular fungal-related parasites of the Bombyx mori, causing the epidemic disease Pebrine and extensive economic losses in the agricultural and sericulture industry. Enterococcus has emerged as one of the predominant gut microorganisms of the major model organism, Bombyx mori. However, the potential interactions mechanism between B. mori, N. bombycis and Enterococcus have not been well demonstrated.

METHODS: To address this gap, we used an insect model, silkworm to examine the potential mechanism of the natural symbiotic bacterium Enterococcus faecalis LX10 drives B. mori refractoriness to N. bombycis infection. E. faecalis LX10 was isolated from the gut of healthy silkworms, and its inhibitory activity against N. bombycis was evaluated at both the cellular and individual levels using posttranslational modifications, gene and protein expression analysis, transfected cells, and in vitro immunofluorescence.

RESULTS: We demonstrated that enterococcin (EntLX), the first antimicrobial protein family in gut commensal bacterium Enterococcus faecalis LX10 of B. mori, contributes to defending against N. bombycis infection resistance depends on the enzyme gelatinase (GelE), disulfide bond and disulfide bond formation proteinA (DsbA). The EntLX protein, abundantly expressed in transgenic BmN cells and gut organs(gut epithelium, peritrophic membrane and contents), can reduce the infection rate of cells and alleviate intestinal damage caused by N. bombycis infection. After simultaneous vaccination with E. faecalis LX10 and N. bombycis, the differentially key metabolites, physiological characteristics(larval mass), or economic traits(cocoon length, cocoon width, whole-cocoon weight, cocoon shell weight, pupation rate and adult emergence rate) showed a certain degrees of recovery and correction compared with those of single N. bombycis inoculation at the individual level.

CONCLUSIONS: This study advances the understanding of the anti-microsporidia activity of enterococci and paves the way for the expression of these molecules as antifungal agents via the genetic transformation of Enterococcus symbionts from disease-transmitting insects.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
*Enterococcus faecalis/metabolism/physiology/genetics
*Bombyx/microbiology/immunology
*Symbiosis
*Nosema/physiology/pathogenicity
*Bacterial Proteins/metabolism/genetics

@article {pmid40382475,
year = {2025},
author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG},
title = {The Microbial Ecology of Antarctic Sponges.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {44},
pmid = {40382475},
issn = {1432-184X},
mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.},
}

*Porifera/microbiology
Animals
Antarctic Regions
*Microbiota
Symbiosis
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Ecosystem
Fungi/classification/genetics/isolation & purification

@article {pmid40381977,
year = {2025},
author = {Ramírez, CS and Tolmie, C and Rivas, MG and Gonzalez, PJ and Murgida, DH and Opperman, DJ and Brondino, CD and Ferroni, FM},
title = {Structural insights into the copper-containing nitrite reductase from Bradyrhizobium japonicum USDA110 and its role in the low nitrite reductase activity of rhizobia.},
journal = {Archives of biochemistry and biophysics},
volume = {},
number = {},
pages = {110467},
doi = {10.1016/j.abb.2025.110467},
pmid = {40381977},
issn = {1096-0384},
abstract = {Bradyrhizobium japonicum USDA110 is a widely used microorganism in the formulation of bioinoculants for soybean crops, harboring a copper-containing nitrite reductase with low enzymatic activity. The activity of BjNirK at pH 6.5 was higher compared to that at pH 8.0, regardless of the presence of either physiological or artificial electron donors. Thermal shift assays reveal that the enzyme is more stable at pH 6.5 than at pH 8.0. X-ray structural data reveals that the funnel for substrate entry shows a wider cavity when compared to other class I NirK structures. Furthermore, the presence of an additional channel for proton provision is observed, in addition to the primary and secondary proton channels. The T2Cu active site can accommodate one or two water molecules, resulting in a tetra- or pentacoordinated metal site, respectively. The structural data correlates well with both optical visible and resonance Raman spectroscopies, denoting a strong blue character of the T1Cu site in both solid and solution states. Furthermore, EPR-monitored redox titration reveals that the catalytic rate is not constrained by T1Cu-T2Cu intraprotein electron transfer reaction at either pH 6.5 or pH 8.0. Additionally, bioinformatics studies indicate that the interaction between the enzyme and the electron donor is not pH dependent. These two observations suggest that the low activity of BjNirK is not caused by inefficient donor-enzyme interaction or impaired electron transfer. The present results suggest that the structural architecture and enzyme properties in rhizobia are designed to ensure low activity, a trait that is particularly advantageous for symbiosis.},
}

@article {pmid40381437,
year = {2025},
author = {Gushi, M and Ishibashi, H and Takayama, K and Yamashiro, H and Takeuchi, I},
title = {Interactive effects of high seawater temperature and the PS II herbicide Irgarol 1051 on photosynthetic efficiency of one species of the Acropora tenuis [sensu lato] complex (Scleractinia: Acroporidae).},
journal = {Marine pollution bulletin},
volume = {218},
number = {},
pages = {118098},
doi = {10.1016/j.marpolbul.2025.118098},
pmid = {40381437},
issn = {1879-3363},
abstract = {Among herbicides, Irgarol 1051 causes the strongest inhibition of maximum effective quantum yield (∆F/Fm') in symbiotic dinoflagellates of corals. In this study, interactive effects of heat stress and Irgarol (1.0 μg/L) were investigated using aquaculture-reared Acropora sp., a species in the Acropora tenuis [sensu lato] complex in southern Japan. Two 7-d experiments were conducted with 27.5 °C as the temperature control and 30.0 or 32.0 °C as heat stress treatments. Coral colour, evaluated by red-green-blue values, and ∆F/Fm' of symbiotic dinoflagellates in coral were monitored daily. In the 27.5 and 30.0 °C treatments, coral colour remained stable throughout the experiment; whereas, corals began to whiten at 32.0 °C in both control and Irgarol treatments. ∆F/Fm' decreased from day 1 in both Irgarol treatments under control (27.5 °C) and heat stress conditions (30.0 and 32.0 °C). In the control treatment, heat stress of 32.0 °C induced a decrease in ∆F/Fm', but less than the decrease in ∆F/Fm' during Irgarol exposure. ∆F/Fm' did not decrease in the temperature control and 30.0 °C heat stress treatments. A significant interactive decrease in ∆F/Fm' was observed on day 1 at both 30.0 and 32.0 °C. Thus, at 30.0 and 32.0 °C, heat stress was considered to accelerate the ∆F/Fm' reduction at the early stage of Irgarol exposure in aquaculture-reared Acropora sp. Compared to our previous study, the present study suggests that the response of corals in the A. tenuis [sensu lato] complex to Irgarol exposure differs depending on the genetic differences, such as species level.},
}

@article {pmid40381311,
year = {2025},
author = {Gao, J and Tian, H and Li, L and Shen, D and Dong, B and Xu, Z},
title = {Two-phase remediation of extreme textured soils: Integrating stabilized sludge and plant-assisted strategies for enhanced water-nutrient supply and nitrogen fixation.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125757},
doi = {10.1016/j.jenvman.2025.125757},
pmid = {40381311},
issn = {1095-8630},
abstract = {The continuous degradation of soil texture has severely suppressed soil productivity. Here, we present a two-phase remediation strategy aimed at improving extreme textured soils (ETS), specifically clay (CL) and sandy (SA) soils, by integrating stabilized sludge (SS) amendment and nitrogen-fixing plant (alfalfa) cultivation. In Phase I, the application of SS improved soil texture, as indicated by the optimized mechanical composition and aggregate structure. Water-stable aggregates contributed to organic carbon accumulation by protecting particulate organics. In addition, the improved aggregate spatial arrangement enhanced water dynamics. In Phase II, alfalfa cultivation restructured the diazotroph community via plant-rhizobium symbiosis, upregulating nitrogenase genes (nifKDH) and boosting nitrogen fixation. The synergy between SS and alfalfa established a resilient microbial ecosystem, offering a sustainable solution for ETS remediation and efficient sludge utilization, addressing both environmental and resource management goals.},
}

@article {pmid40380978,
year = {2025},
author = {Pipes, BL and Nishiguchi, MK},
title = {Generation and validation of a versatile inducible multiplex CRISPRi system to examine bacterial regulation in the Euprymna-Vibrio fischeri symbiosis.},
journal = {Archives of microbiology},
volume = {207},
number = {7},
pages = {147},
pmid = {40380978},
issn = {1432-072X},
support = {EXO 80NSSC18K1053//National Aeronautical and Space Adminstration/ ; EXO 80NSSC18K1053//National Aeronautical and Space Adminstration/ ; DBI-2214028//National Science Foundation/ ; DBI-2214028//National Science Foundation/ ; },
mesh = {*Aliivibrio fischeri/genetics/physiology ; *Symbiosis/genetics ; Animals ; *Gene Expression Regulation, Bacterial ; *CRISPR-Cas Systems ; *Decapodiformes/microbiology ; Genetic Vectors ; Bacterial Proteins/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Plasmids/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {The Vibrio fischeri-Euprymna scolopes symbiosis has become a powerful animal-microbe model system to examine the genetic underpinnings of symbiont development and regulation. Although there has been a number of elegant bacterial genetic technologies developed to examine this symbiosis, there is still a need to develop more sophisticated methodologies to better understand complex regulatory pathways that lie within the association. Therefore, we have developed a suite of CRISPR interference (CRISPRi) vectors for inducible repression of specific V. fischeri genes associated with symbiotic competence. The suite utilizes both Tn7-integrating and shuttle vector plasmids that allow for inducible expression of CRISPRi dCas9 protein along with single-guide RNAs (sgRNA) modules. We validated this CRISPRi tool suite by targeting both exogenous (an introduced mRFP reporter) and endogenous genes (luxC in the bioluminescence producing lux operon, and flrA, the major regulatory gene controlling flagella production). The suite includes shuttle vectors expressing both single and multiple sgRNAs complementary to the non-template strand of multiple targeted genetic loci, which were effective in inducible gene repression, with significant reductions in targeted gene expression levels. V. fischeri cells harboring a version of this system targeting the luxC gene and suppressing the production of luminescence were used to experimentally validate the hypothesis that continuous luminescence must be produced by the symbiont in order to maintain the symbiosis at time points longer than the known 24-h limit. This robust new CRISPRi genetic toolset has broad utility and will enhance the study of V. fischeri genes, bypassing the need for gene disruptions by standard techniques of allelic knockout-complementation-exchange and the ability to visualize symbiotic regulation in vivo.},
}

*Aliivibrio fischeri/genetics/physiology
*Symbiosis/genetics
Animals
*Gene Expression Regulation, Bacterial
*CRISPR-Cas Systems
*Decapodiformes/microbiology
Genetic Vectors
Bacterial Proteins/genetics
Clustered Regularly Interspaced Short Palindromic Repeats
Plasmids/genetics
RNA, Guide, CRISPR-Cas Systems/genetics

@article {pmid40380855,
year = {2025},
author = {Yu, SJ and Shen, R and Lin, DM},
title = {Research advances in the impacts of ectomycorrhizal fungi on the formation and decomposition of soil organic matter in forests.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {3},
pages = {943-949},
doi = {10.13287/j.1001-9332.202503.034},
pmid = {40380855},
issn = {1001-9332},
mesh = {*Mycorrhizae/physiology/metabolism ; *Forests ; *Soil/chemistry ; *Soil Microbiology ; *Organic Chemicals/metabolism/analysis ; Ecosystem ; *Trees/growth & development ; Biodegradation, Environmental ; },
abstract = {Ectomycorrhizal (EcM) fungi are one of the important functional groups of soil fungi, playing a crucial role in the formation, stabilization, and decomposition of soil organic matter (SOM). We summarized the main processes and mechanisms by which EcM fungi contribute to SOM formation, stabilization, and decomposition in forests. Plants allocate a portion of photosynthetic products to symbiotic EcM fungi, which participate in SOM formation by importing them into the soil in the form of mycorrhizal exudates or necromass, whose activities promote the formation of soil aggregate structure and SOM stabilization. EcM fungi decompose SOM directly by secreting extracellular enzymes or by driving the Fenton reaction to generate hydroxyl radicals. They also influence SOM decomposition indirectly by enhancing the activity of saprotrophic fungi (priming effect) or inhibiting their activity (Gadgil effect). The precise quantification of EcM fungi's role in SOM formation remains unclear. Most available studies are concentrated in Europe and North America, but the difference in methodologies makes it difficult to integrate data across regions. Future research should adopt standardized techniques and promote cross-regional collaborative studies. Current understanding of EcM fungi's role in SOM decomposition is mainly based on a few laboratory-cultured species. Future studies should include a broader range of EcM fungal species and investigate their roles in natural environments, particularly in different soil types and forest communities. In addition, the interactions between EcM fungi and saprotrophic fungi have significant impacts on SOM dynamics. Future research should explore the responses of EcM fungi to climate, soil and vegetation in depth to better understand their role in soil carbon cycling.},
}

*Mycorrhizae/physiology/metabolism
*Forests
*Soil/chemistry
*Soil Microbiology
*Organic Chemicals/metabolism/analysis
Ecosystem
*Trees/growth & development
Biodegradation, Environmental

@article {pmid40380241,
year = {2025},
author = {Cheng, G and Kong, W and Lin, R and Jiang, Z and Wang, X and Qin, X and Shi, Y and Yang, P and Chen, X and Xia, L and Xu, Z},
title = {Multi-omics analysis reveals that Bacillus spp. enhance mucosal antiviral immunity in teleost fish by mediating diglyceride production through lipid metabolism.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {123},
pmid = {40380241},
issn = {2049-2618},
mesh = {Animals ; *Bacillus/isolation & purification/genetics/physiology/immunology/classification ; *Lipid Metabolism ; *Fish Diseases/immunology/virology/microbiology ; *Immunity, Mucosal ; *Bass/immunology/microbiology/virology ; Probiotics/administration & dosage ; Microbiota ; Multiomics ; },
abstract = {BACKGROUND: Symbiotic microbiota in vertebrates play critical roles in establishing and enhancing host resistance to pathogenic infections as well as maintaining host homeostasis. The interactions and mechanisms of commensal microbiota-mediated mucosal immune systems have been extensively studied in mammals and, to a lesser extent, in birds. However, despite several studies emphasizing the role of mucosal microbiota in controlling pathogen infections in teleost fish, limited knowledge exists regarding the core microbiota and the mechanisms by which they contribute to resistance against viral infections.

RESULTS: Our findings suggest that viral infections shape clinical manifestations of varying severity in infected fish. An increased abundance of Bacillus spp. in the mild phenotype indicates its crucial role in influencing fish immunity during viral infections. To confirm that Bacillus spp. act as a core contributor against viral infection in fish, we isolated a representative strain of Bacillus spp. from largemouth bass (Micropterus salmoides), which was identified as Bacillus velezensis (Bv), and subsequently conducted feeding trials. Our study demonstrated that dietary supplementation with Bv significantly reduced mortality from largemouth bass virus (LMBV) infection in bass by enhancing host immunity and metabolism as well as by regulating the microbial community. Furthermore, multi-omics analysis elucidated the mechanism by which Bacillus spp. confer resistance to viral infections by regulating the production of diglyceride (DG) during lipid metabolism.

CONCLUSIONS: Our study provides the first evidence that Bacillus spp. are a core microbiota for combating viral infections in teleost fish, shedding light on the conserved functions of probiotics as a core microbiota in regulating microbial homeostasis and mucosal immunity across the vertebrate lineage.},
}

Animals
*Bacillus/isolation & purification/genetics/physiology/immunology/classification
*Lipid Metabolism
*Fish Diseases/immunology/virology/microbiology
*Immunity, Mucosal
*Bass/immunology/microbiology/virology
Probiotics/administration & dosage
Microbiota
Multiomics

@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}

@article {pmid40375452,
year = {2025},
author = {Hutchings, B and López-Legentil, S and Stefaniak, L and Nydam, M and Erwin, PM},
title = {Microbial Distortion? Impacts of Delayed Preservation on Microbiome Diversity and Composition in a Marine Invertebrate.},
journal = {MicrobiologyOpen},
volume = {14},
number = {2},
pages = {e70019},
pmid = {40375452},
issn = {2045-8827},
support = {//This research was supported by the Ruth D. Turner Foundation and National Science Foundation (DEB-2122475)./ ; },
mesh = {Animals ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Urochordata/microbiology ; *Preservation, Biological/methods ; Biodiversity ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Belize ; Time Factors ; DNA, Ribosomal/genetics/chemistry ; Phylogeny ; },
abstract = {Field collections of marine invertebrates are often accompanied by delays in preservation, which may impact microbiome composition. Here, we tested the effects of delayed preservation and relaxation methods on microbiome diversity and composition in the colonial ascidian Trididemnum solidum using 16S rRNA amplicon sequencing. Replicate samples collected from Belizean reefs were either (1) immediately preserved in ethanol ("control"), (2) held in ambient seawater for 3 h before preservation ("SW"), or (3) held in ambient seawater with menthol (a common pre-preservation relaxation technique for ascidian identification) for 3 h before preservation ("SW + M"). All T. solidum microbiomes were different from ambient seawater bacterioplankton and dominated by the same microbial taxa, including the genera Thalassobaculum, Tistrella, and Synechocystis. However, the 3-h delay in sample preservation (SW) significantly reduced microbiome richness compared to controls (p = 0.028), while menthol treatment (SW + M) mitigated this diversity loss (p = 0.208). Microbial composition at the community level did not differ significantly for either delayed preservation method compared to controls (SW p = 0.054, SW + M p = 0.052). Taxon-level shifts were rare but did occur, most notably a bloom of the facultatively anaerobic gammaproteobacterium Catenococcus that was 37x (SW) and 197x (SW + M) more abundant in delayed preservations. After a 3-h preservation delay (SW), only 122 microbial taxa (1.85% of total) exhibited significantly differential abundances with controls, with menthol treatment (SW + M) reducing taxon-level shifts to 65 taxa (0.98%). Our results showed that brief delays in preservation did not significantly alter community-level microbiome composition and dominant taxa, with menthol exposure counteracting minor microbiome shifts associated with preservation delays.},
}

Animals
*Microbiota
RNA, Ribosomal, 16S/genetics
Seawater/microbiology
*Bacteria/classification/genetics/isolation & purification
*Urochordata/microbiology
*Preservation, Biological/methods
Biodiversity
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
Belize
Time Factors
DNA, Ribosomal/genetics/chemistry
Phylogeny

@article {pmid40374873,
year = {2025},
author = {Turner, LD and Raina, JB and Kuzhiumparambil, U and Songsomboom, K and Matthews, JL},
title = {Inhibiting inositol transport disrupts metabolite profiles and mimics heat stress in a model cnidarian-Symbiodiniaceae symbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {755},
pmid = {40374873},
issn = {2399-3642},
mesh = {*Symbiosis ; Animals ; *Heat-Shock Response ; *Inositol/metabolism ; *Dinoflagellida/physiology/metabolism ; *Anthozoa/physiology/metabolism ; *Cnidaria/physiology/metabolism ; Biological Transport ; *Metabolome ; },
abstract = {The nutrient exchange between corals and their symbiotic microalgae (Symbiodiniaceae) is vital for coral survival. Disruptions in this mutualistic relationship, often due to stress-induced dysbiosis, contribute significantly to coral mortality and reef decline globally. Dysbiosis is associated with substantial shifts in various metabolites, notably a rise in inositol, a sugar alcohol, though its role in coral-algae interactions remains unclear. Using a cnidarian model, we identify Symbiodiniaceae as the main source of inositol, with myo- and scyllo-inositol being the dominant forms under normal conditions. During heat stress, scyllo-inositol levels increase by 1.8 times in symbiotic hosts, and up to 26 times in cultured Symbiodiniaceae (Breviolum minutum). Meanwhile, myo-inositol decreases in host tissues but doubles within Symbiodiniaceae, indicating altered nutrient-sharing or stress signalling. In contrast, no changes are observed in aposymbiotic cnidarians (without Symbiodiniaceae). Additionally, inhibiting inositol production and transport in symbiotic tissues disrupts metabolite profiles, mimicking effects seen under heat stress, suggesting that inositol transport is crucial for maintaining metabolic balance and nutrient exchange. These findings reveal that disruptions in inositol dynamics play a critical role in stress responses, offering insights into dysbiosis mechanisms driving coral reef crises.},
}

*Symbiosis
Animals
*Heat-Shock Response
*Inositol/metabolism
*Dinoflagellida/physiology/metabolism
*Anthozoa/physiology/metabolism
*Cnidaria/physiology/metabolism
Biological Transport
*Metabolome

@article {pmid40373376,
year = {2025},
author = {Qiao, X and Zhang, L and Qiu, Z and Wu, Y and Deng, C and Geng, Y and Zhang, Y and Yan, Y and Li, B and Zhang, L and Zhuang, WQ and Yu, K},
title = {Nitrite impairs bioreactor performance due to decreased replication of Candidatus Brocadia sapporoensis by unbalanced energy allocation.},
journal = {Water research},
volume = {283},
number = {},
pages = {123806},
doi = {10.1016/j.watres.2025.123806},
pmid = {40373376},
issn = {1879-2448},
abstract = {The effects of nitrite on anammox activities have been extensively studied. However, the molecular mechanisms of specific microorganisms responding to nitrite in anammox systems remain unexplored. This study investigates how excessive nitrite affects the core metabolisms of AnAOB and symbiotic bacteria, further elucidating the mechanisms by which it regulates microbial growth and nitrogen removal performance. Specifically, the nitrogen removal process in a continuous-flow anammox membrane bioreactor collapsed when the nitrite concentration reached 243 mg N/L. Integrated meta-omics analyses demonstrated that excessive nitrite disrupted the energy metabolism of Ca. Brocadia sapporoensis (AMXB1), reducing the energy available for developing tolerance. Subsequently, it disrupted cell replication by impairing the biosynthesis process of AMXB1, particularly DNA replication and the formation of vital cell structures such as the cell membrane and cell wall, as well as the cellular protection system, leading to the collapse of the anammox system. Additionally, the cross-feeding of amino acids and cofactors between AMXB1 and symbiotic bacteria plays an important role in the recovery of nitrogen removal performance of anammox consortia after nitrite inhibition. The findings provide a novel strategy and direction for improving the tolerance and resilience of anammox consortia in engineered ecosystems.},
}

@article {pmid40373110,
year = {2025},
author = {Park, MJ and Kim, J and Kim, YJ and Yu, J and Jin, H and Woo, S and Zo, YG and Kwon, KK},
title = {Genome-based reclassification of the family Stappiaceae and assessment of environmental forcing with the report of two novel taxa, Flexibacterium corallicola gen. nov., sp. nov., and Nesiotobacter zosterae sp. nov., isolated from coral and seagrass.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322500},
pmid = {40373110},
issn = {1932-6203},
mesh = {Phylogeny ; *Anthozoa/microbiology ; Animals ; *Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Alismatales/microbiology ; },
abstract = {Two novel strains, MaLMAid0302T and SPO723T, isolated from coral and eelgrass, respectively, were distinguished from other Stappiaceae species based on phenotypic, biochemical, phylogenetic, and chemotaxonomic traits. Taxonomic challenges within the family Stappiaceae were addressed using a taxogenomic approach with iterative clustering, establishing an optimal average amino acid identity (AAI) threshold (71.92-72.88%) for genus delineation. This analysis led to major taxonomic revisions, including the establishment of new genera-Parapolycladidibacter, Astericibacter, Flexibacterium, Aliiroseibium, Laciiroseibium, Soliroseibium, Novilabrenzia, Litoriroseibium, and Algilabrenzia-as well as the reassignment of several species: Hongsoonwoonella albiluteola comb. nov., Parapolycladidibacter stylochi gen. nov., comb. nov., Astericibacter flavus gen. nov., comb. nov., Nesiotobacter exalbescens comb. nov., Aliiroseibium hamelinense gen. nov., comb. nov., Laciiroseibium aquae gen. nov., comb. nov., Soliroseibium sediminis gen. nov., comb. nov., Novilabrenzia suaedae gen. nov., comb. nov., Novilabrenzia litorale gen. nov., comb. nov., Litoriroseibium aestuarii gen. nov., comb. nov., Litoriroseibium limicola gen. nov., comb. nov., and Algilabrenzia polysiphoniae gen. nov., comb. nov. Given this extensive taxonomic reclassification of the family Stappiaceae, strain SPO723T (=KCCM 42324T = JCM 14066T) was classified as Nesiotobacter zosterae sp. nov., and Flexibacterium corallicola MaLMAid0302T (=KCTC 92348T = JCM 35474T) was designated as the type species of the newly established genus Flexibacterium. Close phylogenetic ties to Pseudovibrio, known for symbiosis, prompted analysis of niche-specific genetic compositions. Canonical Correspondence Analysis attributed 64% of genomic variation to phylogenetic forcing and 36% to environmental forcing. Functional adaptations included pectin and aromatic compound degradation in sediment strains, nitrogen reduction in flatworm strains, and sulfur metabolism in coral strains. The eelgrass strain exhibited dTDP-L-rhamnose synthesis, potentially aiding biofilm formation for adhesion in dynamic environments. These findings emphasize the roles of both environmental and phylogenetic forcing in shaping genomic diversity and highlight the ecological importance of the family Stappiaceae in marine habitat-associated niches.},
}

Phylogeny
*Anthozoa/microbiology
Animals
*Genome, Bacterial
RNA, Ribosomal, 16S/genetics
*Alismatales/microbiology

@article {pmid40373087,
year = {2025},
author = {Giza, A and Hermanowicz, P and Ważny, R and Domka, A and Rozpądek, P and Łabuz, J},
title = {Effect of UV-A on endophyte colonisation of Arabidopsis thaliana.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323576},
pmid = {40373087},
issn = {1932-6203},
mesh = {*Ultraviolet Rays ; *Arabidopsis/microbiology/radiation effects/genetics/growth & development ; *Endophytes/radiation effects/physiology ; Symbiosis/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; Plant Roots/microbiology/radiation effects ; },
abstract = {UV-A, an important part of sunlight radiation, is typically absent in experiments on plant-endophyte interactions. We examined the impact of UV-A in the 350-400 nm range (UV-A1 waveband) on the plant interactions with fungal endophytes belonging to different taxonomic groups: Paraphoma chrysanthemicola, Phomopsis columnaris, Diaporthe eres, Mucor sp., and yeast Sporobolomyces ruberrimus. Physiologically relevant levels of UV-A did not substantially affect the colonisation of shoots and roots by endophytes. UV-A upregulated the expression of genes involved in the establishment of symbiosis. Specifically, the expression of PDF1.2 was affected by P. chrysanthemicola and S. ruberrimus only under UV-A conditions. Additionally, UV-A exposure upregulated the mRNA levels of ICS1 and PAL1, genes important for plant responses to stress factors. Inoculation with P. chrysanthemicola and S. ruberrimus led to increased expression of the ICS1 gene. We did not observe significant interactions between the effects of UV-A and the presence of endophytes on other examined plant traits, including plant fresh weight, root system architecture, and expression of plant photoreceptor genes. For these physiological parameters, the effects of the presence of endophytes did not depend on UV-A supplementation. Our findings indicate that while UV-A does not substantially influence plant colonisation by the endophytes, it does trigger the upregulation of plant defence genes and affects the shoot growth of Arabidopsis.},
}

*Ultraviolet Rays
*Arabidopsis/microbiology/radiation effects/genetics/growth & development
*Endophytes/radiation effects/physiology
Symbiosis/radiation effects
Gene Expression Regulation, Plant/radiation effects
Plant Roots/microbiology/radiation effects

@article {pmid40372471,
year = {2025},
author = {Lord, KA and Larson, G and Allaby, RG and Karlsson, EK},
title = {A universally applicable definition for domestication.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {22},
pages = {e2413207122},
doi = {10.1073/pnas.2413207122},
pmid = {40372471},
issn = {1091-6490},
mesh = {*Domestication ; Humans ; Animals ; *Biological Evolution ; },
abstract = {The process of domestication is commonly perceived as a human achievement, and domestic species are typically assumed to be those under human control. Domestic species have emerged from a greater diversity of interactions than this perspective allows, and none of the many definitions proposed for domestication can readily, reliably, and consistently distinguish domestic and nondomestic populations. Here, we propose that the process of domestication should instead be defined solely as evolution of a nonhuman population in response to an anthropogenic niche and that a domestic population is one that cannot sustain itself outside of an anthropogenic niche. As a result, this definition does not require comparisons with a presumed and largely unobservable ancestor. Instead, it focuses on the observable relationship between a nonhuman population and humans. It also avoids making assumptions about how domestication happens, thus enabling an exploration of the mechanisms underlying the process of adaptation to an anthropogenic niche. By applying this definition to plants, animals, and microbes, we illustrate its utility for investigating the evolution of the relationship between humans and other species and for anticipating which species are likely to survive in an increasingly human-influenced world. Domestication is simply an evolutionary process resulting from the interaction between two species, one of which is human. As we work to protect Earth's biodiversity, this definition allows us to understand why, in response to the conditions human societies create, some species survive and thrive, while others struggle and go extinct.},
}

*Domestication
Humans
Animals
*Biological Evolution

@article {pmid40371945,
year = {2025},
author = {Roeder, AHK and Bent, A and Lovell, JT and McKay, JK and Bravo, A and Medina-Jimenez, K and Morimoto, KW and Brady, SM and Hua, L and Hibberd, JM and Zhong, S and Cardinale, F and Visentin, I and Lovisolo, C and Hannah, MA and Webb, AAR},
title = {Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants.},
journal = {The Plant cell},
volume = {37},
number = {5},
pages = {},
pmid = {40371945},
issn = {1532-298X},
support = {BB/M011194/1//BBSRC/ ; BB/M015416/1//BBSRC/ ; BB/K011790/1//BBSRC/ ; BB/W001209/1//BBSRC/ ; },
mesh = {*Arabidopsis/genetics/metabolism ; Gene Expression Regulation, Plant ; *Protein Biosynthesis ; },
abstract = {Research in Arabidopsis thaliana has a powerful influence on our understanding of gene functions and pathways. However, not everything translates from Arabidopsis to crops and other plants. Here, a group of experts consider instances where translation has been lost and why such translation is not possible or is challenging. First, despite great efforts, floral dip transformation has not succeeded in other species outside Brassicaceae. Second, due to gene duplications and losses throughout evolution, it can be complex to establish which genes are orthologs of Arabidopsis genes. Third, during evolution Arabidopsis has lost arbuscular mycorrhizal symbiosis. Fourth, other plants have evolved specialized cell types that are not present in Arabidopsis. Fifth, similarly, C4 photosynthesis cannot be studied in Arabidopsis, which is a C3 plant. Sixth, many other plant species have larger genomes, which has given rise to innovations in transcriptional regulation that are not present in Arabidopsis. Seventh, phenotypes such as acclimation to water stress can be challenging to translate due to different measurement strategies. And eighth, while the circadian oscillator is conserved, there are important nuances in the roles of circadian regulators in crop plants. A key theme emerging across these vignettes is that even when translation is lost, insights can still be gained through comparison with Arabidopsis.},
}

*Arabidopsis/genetics/metabolism
Gene Expression Regulation, Plant
*Protein Biosynthesis

@article {pmid40371533,
year = {2025},
author = {Rog, I and Lerner, D and Bender, SF and van der Heijden, MGA},
title = {The Increased Environmental Niche of Dual-Mycorrhizal Woody Species.},
journal = {Ecology letters},
volume = {28},
number = {5},
pages = {e70132},
doi = {10.1111/ele.70132},
pmid = {40371533},
issn = {1461-0248},
support = {TMPFP3_217251//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-088/20//Gebert Rüf Foundation/ ; //Sustainability and Energy Research Initiative Ph.D. Fellowship/ ; },
mesh = {*Mycorrhizae/physiology ; *Symbiosis ; Wood/microbiology ; Phylogeny ; *Ecosystem ; },
abstract = {The presence and distribution of mycorrhizal symbionts can influence plant distribution through specific host-mycorrhiza symbiosis interactions. However, generalist hosts also exist, such as dual-mycorrhizal plants that form symbiotic associations with both ectomycorrhizal fungi (EM) and arbuscular mycorrhizal fungi (AM). Little is known about the effect of dual mycorrhization status on the hosts' global distribution and acclimation to specific environments. This study investigates the potential advantage of dual associations of more than 400 woody genera spread at a global scale. We found that dual-host woody species occupy a broader geographical range and environmental niche space compared to those associating exclusively with either AM or EM. We show that the increased geographic range and expanded environmental niche space are independent of the phylogenetic architecture and evolutionary history of the woody genera. Our results highlight the advantage of generalist host-microbe symbioses between woody species and fungi to expand their range, and their potential role in colonising dry climates.},
}

*Mycorrhizae/physiology
*Symbiosis
Wood/microbiology
Phylogeny
*Ecosystem

@article {pmid40371512,
year = {2025},
author = {Li, L and Sun, Y and Yang, XQ and Fang, HD and Shi, LT and He, GX and Yu, JL and Yan, BG},
title = {[Effects of nitrogen addition on Arachis hypogaea "Qicai"-rhizobia symbiosis and biomass allocation].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {4},
pages = {1109-1117},
doi = {10.13287/j.1001-9332.202504.010},
pmid = {40371512},
issn = {1001-9332},
mesh = {*Nitrogen/pharmacology ; *Symbiosis/physiology ; *Arachis/growth & development/microbiology/physiology ; *Biomass ; *Bradyrhizobium/physiology ; Photosynthesis ; Fertilizers ; },
abstract = {To reveal how rhizobia affects biomass allocation of peanuts under different nitrogen concentrations, we conducted a pot experiment by treatments of Arachis hypogaea "Qicai" with and without Bradyrhizobium inoculation to investigate the characteristics of plant biomass allocation and symbiotic nodulation at the nitrogen addition level of 0, 8, 16, 32, 64 and 128 mmol·L[-1]. The results showed that: 1) Under non-inoculation, the addition of low-level nitrogen (8-32 mmol·L[-1]) had limited impact on plant biomass. When nitrogen addition level reached 64 mmol·L[-1], total plant biomass, leaf biomass, leaf area, and total net photosynthetic rate increased significantly by 82.1%, 116.6%, 116.1% and 122.1% respectively in compared with those without nitrogen addition (0 mmol·L[-1]). 2) Under the condition of inoculation, total plant biomass, leaf biomass, leaf area, and total net photosynthetic rate increased under the nitrogen addition level of 16 mmol·L[-1] by 65.3%, 97.5%, 91.7%, and 112.8%. The nodulation amount of plants and the total amount of leghemoglobin first increased and then decreased with the increases of nitrogen addition level, reaching their maximum values at 49.00 mg·plant[-1] and 0.12 mg·plant[-1] respectively at the nitrogen addition level of 16 mmol·L[-1]. When the nitrogen addition level reached 64 mmol·L[-1], they decreased significantly. There was no nodulation of roots when the nitrogen addition was 128 mmol·L[-1]. 3) Rhizobia inoculation significantly increased leaf biomass, aboveground biomass, leaf area, and total net photosynthetic rate when nitrogen addition level ranged from 8 to 64 mmol·L[-1], with an overall increase of 43.3%, 37.6%, 34.5%, and 53.8% respectively. However, rhizobia inoculation did not affect those indices when the nitrogen addition level was 0 or 128 mmol·L[-1]. Overall, rhizobia inoculation significantly increased the allometric growth constants of leaf-root and leaf-total biomass, and decreased the allometric growth constants of root-stem and root-total biomass. In conclusion, peanuts actively adjust resource allocations among different organs with a trade-off between environmental nitrogen absorption and symbiotic nitrogen fixation, which would maximize the benefit of resource investments. Among the N addition levels involved in this study, 16 mmol·L[-1] is optimal for the symbiotic nodulation of A. hypogaea "Qicai" and Bradyrhizobium.},
}

*Nitrogen/pharmacology
*Symbiosis/physiology
*Arachis/growth & development/microbiology/physiology
*Biomass
*Bradyrhizobium/physiology
Photosynthesis
Fertilizers

@article {pmid40371033,
year = {2025},
author = {Dey, G and Upadhyay, H and Maity, JP and Chen, CY and Wang, SL and Sinha, A and Chakraborty, A},
title = {Root-Associated Plant Growth-Promoting Bacteria in Mangrove Ecosystem and its Application in Sustainable Biotechnology.},
journal = {Indian journal of microbiology},
volume = {65},
number = {1},
pages = {333-346},
pmid = {40371033},
issn = {0046-8991},
abstract = {Mangroves are distinguished as a unique ecotone, characterized by their specialized habitat and extreme environmental conditions, including high salinity, tidal fluctuations, elevated temperatures, low oxygen levels, and waterlogging. While these stressors impose numerous challenges on mangroves, the plants have evolved adaptive mechanisms to cope with such harsh conditions. Crucially, the root-associated microbial community, particularly plant growth-promoting bacteria (PGPB), plays an essential role in aiding mangrove plants to withstand these adverse conditions, highlighting the symbiotic relationship vital for mangrove resilience. The study aims to explore the root-associated PGPB in mangrove ecosystems, focusing on their roles and potential biotechnological applications. It has been found that these diverse PGPB, isolated from mangroves, exhibited plant growth-promoting properties, including nitrogen fixation, solubilization of phosphorus and potassium, and the production of beneficial compounds such as phytohormones, exopolysaccharides, and volatile organic compounds. These traits of PGPB contribute not only to plant growth and development but also to resilience against various stresses, especially salinity. They aid in maintaining nutrient and ionic balance, modulating hormonal levels, providing osmoprotection, mitigating oxidative stress, and enhancing resistance to pathogens within the mangrove ecosystem. Moreover, the study highlights the promising biotechnological applications of these microbes in promoting sustainable agricultural practices in saline environments, enhancing environmental remediation efforts, and supporting mangrove reforestation initiatives. In conclusion, leveraging the symbiotic relationships between mangrove plants and their root-associated PGPB offers innovative, sustainable solutions to contemporary environmental challenges, paving the way for enhanced ecosystem resilience and productivity.},
}

@article {pmid40370212,
year = {2025},
author = {Tekle, YI and Smith, AR and McGinnis, M and Ghebezadik, S and Patel, P},
title = {A New Paramoeba Isolate From Florida Exhibits a Microtubule-Bound Endosymbiont Closely Associated With the Host Nucleus.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e70011},
pmid = {40370212},
issn = {1550-7408},
support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; 2401946//National Science Foundation/ ; 1R15GM116103-02/NH/NIH HHS/United States ; SFA-23-5//Simons Fellow Award/ ; },
mesh = {*Symbiosis ; Phylogeny ; Animals ; Florida ; *Microtubules ; RNA, Ribosomal, 18S/genetics ; DNA, Protozoan/genetics ; },
abstract = {The genera Paramoeba and Neoparamoeba, within the family Paramoebidae (order Dactylopodida), are distinguished by their dactylopodial pseudopodia and the presence of an intracellular eukaryotic symbiont, the Perkinsela-like organism (PLO). Taxonomic classification within these genera has been challenging due to overlapping morphological traits and close phylogenetic relationships. They are marine, with some playing significant roles as parasites. Notably, they have been implicated in sea urchin mass mortality events and are known causative agents of Amoebic Gill Disease (AGD) in fish. Despite their ecological and economic importance, many aspects of their diversity, biology, evolution, and host interactions remain poorly understood. In this study, we describe a novel amoeba species, Paramoeba daytoni n. sp., isolated from Daytona Beach, Florida. Morphological and molecular analyses confirm its placement within the Paramoeba clade, closely related to P. eilhardi, P. karteshi, and P. aparasomata. Phylogenetic assessments using 18S rDNA (18S) and Cytochrome c Oxidase I (COI) markers demonstrate the limitations of the 18S gene for species delineation, highlighting COI as a more reliable genetic marker for this group. Additionally, observations on PLO morphology, movement, and microtubule association provide insights into the endosymbiotic relationship, reinforcing the need for further research into this unique eukaryote-eukaryote symbiosis.},
}

*Symbiosis
Phylogeny
Animals
Florida
*Microtubules
RNA, Ribosomal, 18S/genetics
DNA, Protozoan/genetics

@article {pmid40369997,
year = {2025},
author = {Zhao, Z and Wang, Y and Yang, L and Qian, X and Yang, A and Liu, J and Jacquemyn, H and Li, T and Xing, X},
title = {Metabolic Shifts and Nutrient Transfer Patterns in Orchid Seeds During Symbiotic Germination.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15612},
pmid = {40369997},
issn = {1365-3040},
support = {//This study was supported by the National Natural Science Foundation of China (Grant No. 32170013), the CAMS Initiative for Innovative Medicine (Grant No. 2021-I2M-1-031), the Science and Technology Program of the Xizang Autonomous Region (Grant No. XZ202402ZD0002), and the Science and Technology Program of the Inner Mongolia Autonomous Region (Grant No. 2023YFDZ0076)./ ; },
abstract = {Symbiotic germination in orchids is a complex biological process driven by a unique dependence on mycorrhizal fungi. It is generally assumed that, due to a lack of endosperm, orchids fully rely on fungi for carbon sources. However, orchid seed embryos store substantial nutrient reserves, but the metabolic functions of these reserves and their roles in establishing symbiosis during germination remain unclear. Here, we used time-series transcriptomics and ultrastructural morphological analyses to investigate the early stages of symbiotic germination in Gymnadenia conopsea, a terrestrial orchid widely distributed across Eurasia. We identify three distinct phases during early seed germination (seed imbibition, fungal invasion and symbiotic establishment) that correspond with pronounced changes in gene expression and energy metabolism. During imbibition, lipid metabolism was already active, leading the oleosomes to fuse into large lipid vacuoles, whereas carbohydrate metabolism became dominant after fungal invasion, with lipid droplets appearing within fungal hyphae. Based on this transcriptomic and morphological evidence, we propose a potential model in which lipid vacuoles facilitate lipid transfer from the seeds to the fungi during the initial invasion, after which the fungi supply carbohydrates to the seeds for further development.},
}

@article {pmid40369072,
year = {2025},
author = {Yang, T and Hu, X and Cao, F and Yun, F and Jia, K and Zhang, M and Kong, G and Nie, B and Liu, Y and Zhang, H and Li, X and Gao, H and Shi, J and Liang, G and Hu, G and Kasper, DL and Song, X and Qian, Y},
title = {Targeting symbionts by apolipoprotein L proteins modulates gut immunity.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40369072},
issn = {1476-4687},
abstract = {The mammalian gut harbours trillions of commensal bacteria that interact with their hosts through various bioactive molecules[1,2]. However, the mutualistic strategies that hosts evolve to benefit from these symbiotic relationships are largely unexplored. Here we report that mouse enterocytes secrete apolipoprotein L9a and b (APOL9a/b) in the presence of microbiota. By integrating flow cytometry sorting of APOL9-binding bacterial taxa with 16S ribosomal RNA gene sequencing (APOL9-seq), we identify that APOL9a/b, as well as their human equivalent APOL2, coat gut bacteria belonging to the order of Bacteroidales with a high degree of specificity through commensal ceramide-1-phosphate (Cer1P) lipids. Genetic abolition of ceramide-1-phosphate synthesis pathways in gut-dominant symbiote Bacteroides thetaiotaomicron significantly decreases the binding of APOL9a/b to the bacterium. Instead of lysing the bacterial cells, coating of APOL9a/b induces the production of outer membrane vesicles (OMVs) from the target bacteria. Subsequently, the Bacteroides-elicited outer membrane vesicles enhance the host's interferon-γ signalling to promote major histocompatibility complex class II expression in the intestinal epithelial cells. In mice, the loss of Apol9a/b compromises the gut major histocompatibility complex class II-instructed immune barrier function, leading to early mortality from infection by intestinal pathogens. Our data show how a host-elicited factor benefits gut immunological homeostasis by selectively targeting commensal ceramide molecules.},
}

@article {pmid40368875,
year = {2025},
author = {Zhang, X and Ma, J and Zhang, P and Shi, W and Zou, R and Kohler, A and Yang, Y and Martin, FM and Zhang, F},
title = {Functional characterization of the N assimilation pathways in the mycelium of Laccaria bicolor and the ectomycorrhizal symbiosis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf194},
pmid = {40368875},
issn = {1532-2548},
abstract = {Ectomycorrhizal (ECM) fungi contribute to N, Pi, and water uptake in trees while obtaining carbohydrates from their host plants. However, the molecular mechanisms underlying N assimilation during ECM symbiosis remain unclear. In this study, we used RNA interference (RNAi) to silence the expression of genes encoding glutamine synthetase (GS) and NADP-glutamate dehydrogenase (GDH), which are key enzymes involved in N assimilation in the ectomycorrhizal basidiomycete, Laccaria bicolor. LbGS and LbGDH RNAi strains exhibited significantly reduced mycelial growth when cultivated with various inorganic N sources. Compared to the wild-type mycelium, the RNAi strains demonstrated a reduced formation rate of ECM rootlets, indicating the essential role of these two enzymes in the establishment of symbiosis. Transcriptomic analysis revealed that silencing of LbGS and LbGDH also altered the expression of other genes involved in N metabolism in ECM rootlets. 15N and 13C tracer experiments demonstrated that LbGS silencing affects carbon exchange in ECM roots. Our findings have established that both GS and NADP-GDH pathways play crucial roles in N assimilation in free-living mycelia and ECM roots, although the GS/GOGAT pathway appears to be predominant.},
}

@article {pmid40368494,
year = {2025},
author = {Pate, K and Linder, JM and Passwater, C and Harrelson, S and Cochran, A},
title = {Exploration of Clinical Nurse Specialist Preceptors' Perception of Competencies.},
journal = {Journal of professional nursing : official journal of the American Association of Colleges of Nursing},
volume = {58},
number = {},
pages = {39-45},
doi = {10.1016/j.profnurs.2025.02.008},
pmid = {40368494},
issn = {1532-8481},
mesh = {Humans ; *Preceptorship ; *Nurse Clinicians/psychology ; *Clinical Competence ; Male ; Female ; Adult ; North Carolina ; Middle Aged ; Surveys and Questionnaires ; Students, Nursing/psychology ; },
abstract = {BACKGROUND: Despite the importance of preceptors in guiding role transitions, limited literature exists on the clinical nurse specialist (CNS) preceptor to support a symbiotic relationship with CNS students.

PURPOSE: The aim of the study was to explore CNS preceptors' perceptions of their competencies.

METHODS: A descriptive correlational design was utilized in a convenience sample of CNS preceptors across the state of North Carolina, measuring competency with the Preceptor Self-Assessment Tool (PSAT)-40 in three competency domains: interpersonal and intrapersonal skills and attitudes, knowledge and understanding, and administrative resources and support.

RESULTS: The majority of preceptors reported scores in the advanced and proficient range on all three domains, with the administrative resources and support domain demonstrating the lowest scores. The knowledge and understanding domain demonstrated statistically significant correlations with the highest degree held, years of CNS experience, number of CNS students precepted, and recency of last precepting experience. Both years of experience as a nurse and CNS demonstrated statistically significant correlations with the total score, with multivariate analysis also supporting CNS experience.

CONCLUSIONS: Better understanding CNS preceptor competencies aids in appropriate preceptor selection as well as supports the development and implementation of professional development opportunities to prepare individuals acclimating to the preceptor role.},
}

Humans
*Preceptorship
*Nurse Clinicians/psychology
*Clinical Competence
Male
Female
Adult
North Carolina
Middle Aged
Surveys and Questionnaires
Students, Nursing/psychology

@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}

@article {pmid40366931,
year = {2025},
author = {Romagnoli, MG and Catania, MDV and Arana, MD and Albornoz, PL},
title = {Ectomycorrhizas in Lycopodiopsida: their first registry and arbuscular mycorrhiza in Phlegmariurus saururus (Huperziaceae).},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {2},
pages = {e20241248},
doi = {10.1590/0001-3765202520241248},
pmid = {40366931},
issn = {1678-2690},
mesh = {*Mycorrhizae/classification/physiology/isolation & purification ; *Plant Roots/microbiology ; Symbiosis/physiology ; },
abstract = {Lycophytes show no instances of ectomycorrhizas. Phlegmariurus saururus is the only Huperziaceae that grows in Comechingones biogeographic province, in sunny, exposed surficial rock crevices with poor soil development and very scarce water. As mycorrhizas improve plant fitness in natural ecosystems, it was hypothesized that P. saururus can develop multiple types of fungal symbiosis, including ectomycorrhizas. For detecting, identification and description of mycorrhizas, conventional techniques were employed, and samples of roots were cut with an ultra-microtome to obtain thin (3 µm) and ultrathin (0.1 µm) sections. Phlegmariurus saururus is the first species of Lycopodiopsida where the ectomycorrhizas are evidenced. Arbuscular mycorrhizas and septate endophytes were also found. Ectomycorrhizas can alter the anatomy and hydrophilic properties of roots, improving the adaptation of the plant hosts to habitats with a marked period of drought, as the novel Andean Comechingones habitats. The ectomycorrhizas detected in P. saururus could be considered as an adaptive mechanism related to the successful colonisation of this habitat and can undergo a significant transformation in the lifestyle of fungal symbiosis of lycophytes, which could provide important insights into this morphological and functional evolution.},
}

*Mycorrhizae/classification/physiology/isolation & purification
*Plant Roots/microbiology
Symbiosis/physiology

@article {pmid40366182,
year = {2025},
author = {Martin Říhová, J and Vodička, R and Hypša, V},
title = {An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022025},
doi = {10.1128/aem.00220-25},
pmid = {40366182},
issn = {1098-5336},
abstract = {The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.},
}

@article {pmid40366159,
year = {2025},
author = {Esin, JJ and Visick, KL and Kroken, AR},
title = {Calcium signaling controls early stage biofilm formation and dispersal in Vibrio fischeri.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0007725},
doi = {10.1128/jb.00077-25},
pmid = {40366159},
issn = {1098-5530},
abstract = {UNLABELLED: Bacterial dispersal from a biofilm is presently the least-studied step of the biofilm life cycle. The symbiotic bacterial species Vibrio fischeri is a model organism for studying biofilms relevant to a eukaryotic host; however, methodology is lacking to readily study the dispersal of this microbe from biofilms formed in the lab. Here, we adapted a time-lapse assay to visualize biofilm dispersal by V. fischeri. We observed biofilm formation and dispersal for multiple V. fischeri isolates, which displayed a variety of biofilm architecture phenotypes and dispersal dynamics. We then investigated V. fischeri strain ES114 using genetic tools and mutants available for this strain. ES114 exhibited calcium-dependent biofilm formation followed by a rapid (less than 10 min) coordinated dispersal event that occurred approximately 5 h from the experimental start. Biofilm dispersal was largely independent of the dispersal-promoting protease encoded by lapG. Although we found no role under our conditions for either biofilm formation or dispersal for several other factors including polysaccharides and autoinducers, we determined that biofilm formation was enhanced, and dispersal was delayed, with increased concentrations of calcium. Furthermore, biofilm formation depended on the calcium-responsive diguanylate cyclase (DGC) CasA, and dispersal could be modulated by overexpressing CasA. Our work has thus developed a new tool for the V. fischeri field and uncovered a key role for calcium signaling and c-di-GMP in early biofilm formation and dispersal in V. fischeri.

IMPORTANCE: Biofilm formation and dispersal are critical steps in both symbiotic and pathogenic colonization. Relative to biofilm formation, the process of dispersal in the model symbiont Vibrio fischeri, and other bacteria, is understudied. Here, we adapted an imaging assay to study early biofilm formation and the dispersal process in V. fischeri. We demonstrated that our assay can quantify biofilm formation and dispersal over time, can reveal phenotypic differences in diverse natural wild-type isolates, and is sensitive enough to investigate the impact of environmental factors. Our data confirm that calcium is a potent biofilm formation signal and identify the diguanylate cyclase CasA as a key regulator. This work leads the way for more in-depth research about unknown mechanisms of biofilm dispersal.},
}

@article {pmid40365791,
year = {2025},
author = {Howard, NOA and Rodriguez-Morelos, VH and Allen, L and Chinoruma, P and Cohen, LD and Hoysted, GA and Jungblut, AD and Lamb, I and Moeskjaer, S and Pinzari, F and Prout, J and Stanley, CE and Ton, J and Watts, A and Williams, A and Daniell, T and Wanke, A and Schornack, S and Pressel, S and Field, KJ},
title = {What's in a name? The case for standardised nomenclature for mutualistic Mucoromycotina 'fine root endophytes'.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf210},
pmid = {40365791},
issn = {1460-2431},
}

@article {pmid40365728,
year = {2025},
author = {Venn, AA and Tambutté, E and Crovetto, L and Tambutté, S},
title = {pH regulation in coral photosymbiosis and calcification: a compartmental perspective.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70200},
pmid = {40365728},
issn = {1469-8137},
support = {//Government of the Principality of Monaco/ ; },
abstract = {The coral-dinoflagellate photosymbiosis and coral calcification underpin shallow water, coral reef ecosystems. This review examines the pivotal role of pH regulation in the cell physiology of these processes. Despite simple tissue organization, photosymbiotic corals maintain a complex internal microenvironment, with distinct compartments exhibiting contrasting pH levels. For example, the acidic 'symbiosome' surrounds the algal symbionts, while the alkaline 'extracellular calcifying medium' occurs at the growing front of the skeleton. We discuss how pH regulation of these compartments is crucial to the functioning of coral photosymbiosis and calcification, as well as mitigating the internal acid-base imbalances that these processes create. The role of pH regulation in the interplay between photosymbiosis and calcification is also discussed, focusing on the influence of symbiont photosynthesis on transepithelial gradients and the distribution of energy sources in the coral colony. Throughout this review, insights into pH regulation derived from previous research on ocean acidification are integrated to deepen understanding. Finally, we propose research priorities to advance knowledge of coral resilience under changing ocean conditions, such as investigating inorganic carbon concentration within coral compartments, species-specific differences and the impacts of thermal stress on pH regulation.},
}

@article {pmid40364482,
year = {2025},
author = {Li, Q and Imran, },
title = {Using biochar, compost, and dry-based organic amendments in combination with mycorrhizae for mitigating heavy metal contamination in soil.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/15226514.2025.2502458},
pmid = {40364482},
issn = {1549-7879},
abstract = {Water scarcity has led to the increased use of untreated wastewater for irrigation, contributing to heavy metal (HM) accumulation in soils and crops. This study evaluated the effectiveness of organic amendments and arbuscular mycorrhizal fungi (AMF) in reducing HM bioavailability and enhancing plant growth. A two-year pot experiment (2022-2023) was conducted using eight treatments (T1-T8) and three replicates each. Treatments included: T1 (Control), T2 Rice straw, T3, rice straw compost, T4, rice straw biochar, T5, AMF, T6, Straw + AMF, T7, compost + AMF, and T8, biochar + AMF. Post-harvest analysis showed that T7 and T8 significantly reduced soil and plant HM levels. T8 was the most effective, reducing Pb, Cd, and Ni in grains by up to 93%, 76%, and 83%, respectively. Shoot HM concentrations declined by 22%-52%, and grain uptake dropped by 58%-92%. T8 also improved shoot and root dry weights by 66% and 48%, and grain yield by 56%. Root colonization and mycorrhizal intensity increased significantly, along with urease (78%) and catalase (156%) activities. Results highlight the potential of T8 (biochar + AMF) as a sustainable strategy for remediating contaminated soils and improving crop productivity.},
}

@article {pmid40363828,
year = {2025},
author = {Tuani, YT and Ayon, NJ and Onjiko, RM and Choi, SB and Yadav, S and Eleftherianos, I and Nemes, P},
title = {Capillary Electrophoresis Electrospray Ionization Mass Spectrometry Reveals Metabolic Perturbations During Nematode Infection in Drosophila melanogaster.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
doi = {10.3390/molecules30092023},
pmid = {40363828},
issn = {1420-3049},
support = {IOS 2019869//NSF/ ; },
mesh = {Animals ; *Spectrometry, Mass, Electrospray Ionization/methods ; Electrophoresis, Capillary/methods ; *Drosophila melanogaster/parasitology/metabolism/microbiology ; Metabolome ; Metabolomics/methods ; *Nematode Infections/metabolism/parasitology ; Larva/metabolism/parasitology ; },
abstract = {Drosophila melanogaster is broadly used to model host-pathogen interactions. Entomopathogenic nematodes are excellent research tools for dissecting the molecular and functional basis of parasitism and the host's anti-parasitic response. In this work, we used discovery metabolomics to explore the differences in the metabolome composition of wild type D. melanogaster larvae that were infected with symbiotic nematodes (Steinernema carpocapsae carrying Xenorhabdus nematophila mutualistic bacteria) or axenic nematodes (S. carpocapsae lacking their bacterial partners). Benefiting from their high separation power, sensitivity, and compatibility with low amounts of the starting metabolome, we leveraged microanalytical capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS) to profile the small (<500 Da) polar portion of the metabolome among these experimental treatments. We detected and quantified 122 different small molecules, of which 50 were identified with high confidence. Supervised multivariate analysis revealed that the infection was paralleled with changes in amino acid biosynthesis (arginine, phenylalanine, tryptophan, and tyrosine), metabolism (alanine, arginine, aspartate, glutamate, glycine, proline, serine, and threonine), and classical signalling (aspartate, γ-aminobutyrate, glutamate, and pyridoxine). This study demonstrates the ability of high-sensitivity CE-ESI-MS to uncover metabolic perturbations during infection. The results from the metadata may facilitate the design of targeted studies to explore small biomolecules and their functions during host-pathogen interaction.},
}

Animals
*Spectrometry, Mass, Electrospray Ionization/methods
Electrophoresis, Capillary/methods
*Drosophila melanogaster/parasitology/metabolism/microbiology
Metabolome
Metabolomics/methods
*Nematode Infections/metabolism/parasitology
Larva/metabolism/parasitology

@article {pmid40363747,
year = {2025},
author = {Grondalska, J and Kolniak-Ostek, J},
title = {Evaluation of Anti-Inflammatory, Antidiabetic, Antioxidant, and Anticholinergic Activities, as Well as Chemical Composition and Polyphenolic Compounds in Novel SCOBY-Fermented Juices.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
doi = {10.3390/molecules30091940},
pmid = {40363747},
issn = {1420-3049},
mesh = {*Polyphenols/chemistry/pharmacology/analysis ; *Antioxidants/pharmacology/chemistry ; *Fruit and Vegetable Juices/analysis ; *Anti-Inflammatory Agents/pharmacology/chemistry ; *Hypoglycemic Agents/pharmacology/chemistry ; Fermentation ; Malus/chemistry ; },
abstract = {Fermentation processes, which occur under the influence of multiplying microorganisms, lead to the creation of products with beneficial health properties. Due to the growing interest of consumers in beverages with health-promoting properties, new raw materials and their processing methods are being intensively studied to obtain products with improved functional values. The purpose of the study is to determine the effect of fermentation using SCOBY (Symbiotic Culture of Bacteria and Yeast) on the chemical composition, polyphenolic profile, and biological activity of apple and pear juices. The fermentation process caused a decrease in the content of polyphenols in apple juice from 1568.8 to 1269.0 mg/L, while in pears, an increase was observed from 492.9 to 576.7 mg/L. Statistically significant changes were observed in the content of individual groups of polyphenolic compounds. The fermentation process also influenced the increase in the value of anti-inflammatory, antioxidant, antidiabetic, and anticholinergic activity. This indicates that fermentation can be an effective process in increasing the biological properties of fruit juices. This fact can be used in the prevention of lifestyle diseases and in the production of functional foods with targeted health-promoting properties.},
}

*Polyphenols/chemistry/pharmacology/analysis
*Antioxidants/pharmacology/chemistry
*Fruit and Vegetable Juices/analysis
*Anti-Inflammatory Agents/pharmacology/chemistry
*Hypoglycemic Agents/pharmacology/chemistry
Fermentation
Malus/chemistry

@article {pmid40362462,
year = {2025},
author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R},
title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
pmid = {40362462},
issn = {1422-0067},
support = {xxxxx//AFRRI/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; },
abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.},
}

Animals
Male
Female
Mice
*Metabolomics/methods
*Metagenomics/methods
*Radiation, Ionizing
*Colon/radiation effects/metabolism/microbiology
*Gastrointestinal Microbiome/radiation effects
Sex Factors
Whole-Body Irradiation/adverse effects
Mice, Inbred C57BL

@article {pmid40361629,
year = {2025},
author = {Andrade, DKA and Wang, B and Lima, EMF and Shebeko, SK and Ermakov, AM and Khramova, VN and Ivanova, IV and Rocha, RDS and Vaz-Velho, M and Mutukumira, AN and Todorov, SD},
title = {Kombucha: An Old Tradition into a New Concept of a Beneficial, Health-Promoting Beverage.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091547},
pmid = {40361629},
issn = {2304-8158},
support = {grants 2023/05394-9; 2024/01721-8; 2024/13311-9//FAPESP, Brazil/ ; UIDB/05937/2020 and UIDP/05937/2020//Fundação para a Ciência e a Tecnologia (FCT), Portugal, for funding CISAS/ ; EGISU R&D No. FZNE-2024-0013//Russian Federation/ ; },
abstract = {Kombucha is an ancient, fermented beverage that has gained increasing popularity worldwide due to its potential health benefits. Its origins trace back to China, from where it spread across Asia and Europe before reaching the modern global market. The fermentation of kombucha is mediated by a Symbiotic Culture of Bacteria and Yeasts (SCOBY), comprising yeasts, acetic acid bacteria, and lactic acid bacteria. The microbial consortium plays a crucial role in the production of organic acids and bioactive metabolites, shaping the sensory characteristics of the beverage. Given the growing interest in kombucha as a functional beverage, this study aims to explore its historical background, fermentation process, and microbiological composition, including key yeasts, acid acetic bacteria, and lactic acid bacteria and their interactions. Additionally, we describe the potential health effects of kombucha, particularly its antimicrobial and antioxidant activity, the probiotic potential of the strains associated with kombucha, and safety considerations while also addressing the risks associated with its consumption. Although several studies suggested that kombucha may have antioxidants, antimicrobial, and probiotic properties, as well as contribute to gut microbiota regulation and immune system support, there is significant variability in the composition of the beverage, especially in artisanal preparations. This variability poses challenges in standardizing its potential effects and ensuring consistent safety. The risk of contamination further underscores the importance of adhering to strict sanitary production standards. To scientifically validate its health benefits and guarantee safe consumption, further research with larger sample sizes and robust methodologies is essential. The findings of this study will contribute to a deeper understanding of the functional properties of kombucha and provide scientific support for its safe and beneficial applications.},
}

@article {pmid40361556,
year = {2025},
author = {Li, J and Wu, J and Tu, M and Xiao, X and Hu, K and Li, Q and Zhao, N and Liu, A and Ao, X and Hu, X and Liu, S},
title = {Interaction Between Lactic Acid Bacteria and Acetic Acid Bacteria in Sichuan Bran Vinegar: Impact on Their Growth and Metabolites.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091471},
pmid = {40361556},
issn = {2304-8158},
support = {2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; },
abstract = {Microbial interactions are essential for maintaining the stability and functionality of microbiota in fermented foods. In this study, representative strains of predominant lactic acid bacteria and acetic acid bacteria in Sichuan bran vinegar were selected, and their interactions in a simulated solid-state fermentation system were investigated. The results reveal that the biomass of A. pasteurianus LA10 significantly increased in both the co-culture and the pure culture, whereas the biomass of L. amylovorus LL34 in the co-culture (6.44 ± 0.30 lg CFU/g) was significantly lower than that in the pure culture (7.28 ± 0.30 lg CFU/g) (p < 0.05), indicating a partially harmful symbiosis between these two strains. The metabolic analysis shows that total acid (21.82 mg/g) and acetic acid (9.53 mg/g) contents in the co-culture were lower than those in the pure culture of LA10, suggesting that LL34 inhibited the acid-producing activity of LA10 to some extent. The interaction between the two bacteria also influenced the production of volatile compounds and non-volatile compounds, as revealed by GC-MS and untargeted UHPLC-MS/MS, respectively. Significant enrichment of acid and amino acid metabolism pathways was observed in the co-culture, revealing the impact of bacterial interactions on flavor development. This study provides valuable insights into the advancement of vinegar brewing technology.},
}

@article {pmid40360784,
year = {2025},
author = {Voolstra, CR and Schlotheuber, M and Camp, EF and Nitschke, MR and Szereday, S and Bejarano, S},
title = {Spatially restricted coral bleaching as an ecological manifestation of within-colony heterogeneity.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {740},
pmid = {40360784},
issn = {2399-3642},
support = {468583787//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; *Coral Bleaching ; Symbiosis ; Ecosystem ; Dinoflagellida/physiology ; },
abstract = {Coral bleaching is a widespread stress response of reef-building corals to elevated sea temperatures, resulting in the loss of symbiotic algae and often leading to coral death and reef degradation. Although coral bleaching occurs globally, not all reefs, species, colonies, or polyps bleach equally. Understanding intra-colony bleaching heterogeneity is crucial to anticipate the extent of coral loss at 2°C warming and harness variability to inform restorative interventions. Partially bleached coral colonies are commonly documented yet rarely tracked to determine whether they reflect ecologically distinct heterogeneity (e.g., in thermal tolerance) or eventually bleach completely. Focusing on bleaching that appears restricted to certain areas within a coral colony, we examine its putative basis in the spatial variability of the holobiont. A coral's three-dimensional structure creates mosaics of microenvironments. Adaptations to these microenvironments are underpinned by intra-colony differences in Symbiodiniaceae association, microbiome assemblage, and nutritional status, giving rise to microhabitats. Genetic mosaicism and epigenetic changes further contribue to intra-colony phenotypic heterogeneity. We pinpoint methodologies to align spatially restricted bleaching to different forms of coral surface heterogeneity, examine the common assumption that coral fragments represent entire colonies, and illuminate implications for coral biology and restoration.},
}

Animals
*Anthozoa/physiology/microbiology
Coral Reefs
*Coral Bleaching
Symbiosis
Ecosystem
Dinoflagellida/physiology

@article {pmid40359357,
year = {2025},
author = {Zhao, X and Hou, X and Zhou, W and Yan, H and Wen, H and Jiang, H and Tan, L},
title = {Variation of [239,240]Pu in Coral and Its Response to the Climate System in South China Sea.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02025},
pmid = {40359357},
issn = {1520-5851},
abstract = {With the acceleration of climate change, understanding the behavior of the anthropogenic radioactive substances─particularly their responses to the climate system─has become critical for assessing their transport, transfer, and impact on the ecosystems. However, this remains underexplored, particularly in the South China Sea (SCS), where radioactivity is derived from both the close-in fallout of the Pacific Proving Ground (PPG) and the global fallout. Additionally, this region is quite sensitive to climate change. A coral core collected from Xisha Island, SCS, was initially analyzed for high-radiotoxicity [239,240]Pu. Approximately 72-84% of plutonium in coral originated from the close-in fallout of PPG through ocean current compared to the direct global fallout. However, the [239,240]Pu concentration still remains in background levels and does not show a significant radiation risk. After 1980, a distinct pattern emerged characterized by a "higher" concentration but a "lower" [240]Pu/[239]Pu atom ratio compared to the levels in the open west Pacific. This is primarily attributed to the seasonal upwelling of subsurface seawater on the continental shelf of SCS, driven by the prevailing southwest monsoon. Significantly elevated [239,240]Pu concentrations were observed during typical ENSO years 1983, 1988, and 1997. This is due to the elevated temperature, coral bleaching, and expulsion of symbiotic zooxanthellae. After expulsion, zooxanthellae containing higher [239,240]Pu compared to skeleton rapidly die, and their debris directly deposit onto the coral skeleton, in contrast to the metabolic way of [239,240]Pu during normal years. This finding offers critical insights into ecosystem protection in SCS amid global changes and the potential threat of nuclear contamination.},
}

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods

@article {pmid40358698,
year = {2025},
author = {Hasali, NHM and Shahbaz, M and Seelan, JSS and Ibrahim, NA and Wiart, C and Arumugam, N and Salam, MA and Musthafa, MM and Appalasamy, S},
title = {Endophytes of Zingiberaceae: distribution and bioactivity of their bioactive metabolites.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {145},
pmid = {40358698},
issn = {1432-072X},
mesh = {*Endophytes/metabolism/chemistry ; *Zingiberaceae/microbiology ; Anti-Bacterial Agents/pharmacology ; Plant Growth Regulators/metabolism ; Bacteria/metabolism ; Anti-Infective Agents/pharmacology ; },
abstract = {The endophytes associated with the Zingiberaceae family have demonstrated remarkable potential in various biological activities through their bioactive compounds that are useful for both medical and agricultural purposes. Additionally, isolated secondary metabolites from symbiotic microbes associated with this family of plants have shown promising results in various biological activities such as antifungal, anticancer, antidiabetic, anti-inflammatory, and antibacterial. This review focuses on the bioactive metabolites of Zingiberaceae endophytes with their potential biological activities against different pathogens as well as the production of phytohormones that promote plant growth. Furthermore, bibliometric analysis revealed the current key trends and collaborative works in this field. Additionally, the bibliometric analysis also explored a total of 75 relevant publications from the Scopus database that India is the most contributing country in this field with 38.7% of the total reported research work. The bibliometric approach helps uncover new research gaps by identifying emerging trends, underexplored topics, and collaborative networks, providing insights into areas that require further investigation and development. Notably, Streptomyces spp. have been commonly reported as potent endophytes, generating bioactive substances such as Vanillin and Resacetophenone with strong antibacterial activities. Significant knowledge gaps still exist, and with evolving therapeutic potential, this could offer a wide opportunity for new studies to emerge.},
}

*Endophytes/metabolism/chemistry
*Zingiberaceae/microbiology
Anti-Bacterial Agents/pharmacology
Plant Growth Regulators/metabolism
Bacteria/metabolism
Anti-Infective Agents/pharmacology

@article {pmid40357979,
year = {2025},
author = {Ntiri, ES and Chun Nin Wong, A},
title = {Microbial metabolites as engines of behavioral variation across animals.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2501191},
doi = {10.1080/19490976.2025.2501191},
pmid = {40357979},
issn = {1949-0984},
mesh = {Animals ; *Behavior, Animal/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism/genetics/classification ; Vertebrates/physiology/microbiology ; Invertebrates/physiology/microbiology ; Humans ; Circadian Rhythm ; Signal Transduction ; },
abstract = {The microbiome, especially that present in the gut, has emerged as a key modulator of animal behavior. However, the extent of its influence across species and behavioral repertoires, as well as the underlying mechanisms, remains poorly understood. Increasing evidence suggests that microbial metabolites play an important role in driving behavioral variation. In this review, we synthesize findings from vertebrates to invertebrates, spanning both model and non-model organisms, to define key groups of microbial-derived metabolites involved in modulating seven distinct behaviors: nutrition, olfaction, circadian rhythms, reproduction, locomotion, aggression, and social interactions. We discuss how these microbial metabolites interact with host chemosensory systems, neurotransmitter signaling, and epigenetic modifications to shape behavior. Additionally, we highlight critical gaps in mechanistic understanding, including the need to map additional host receptors and signaling pathways, as well as the untapped potential of microbial biosynthetic gene clusters as sources for novel bioactive compounds. Advancing these areas will enhance understanding of the microbiome's role in behavioral modulation and open new avenues for microbiome-based interventions for behavioral disorders.},
}

Animals
*Behavior, Animal/physiology
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism/genetics/classification
Vertebrates/physiology/microbiology
Invertebrates/physiology/microbiology
Humans
Circadian Rhythm
Signal Transduction

@article {pmid40357892,
year = {2025},
author = {Neubauer, A and Iniesta-Pallarés, M and Álvarez, C and Bailly, A and Szövényi, P and Mariscal, V},
title = {Quantitative Assessment of Hormogonia Induction in Nostoc punctiforme by a Fluorescent Reporter Strain.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf197},
pmid = {40357892},
issn = {1460-2431},
abstract = {While symbiotic plant-cyanobacteria interactions hold significant potential for revolutionizing agricultural practices by reducing the application of artificial nitrogen fertilizers, the genetic underpinnings of the symbiotic interaction between the plant host and the cyanobiont remain poorly understood. In particular, the molecular mechanisms through which host plants induce the formation of motile cyanobacterial filaments (hormogonia), essential for colonization and initiation of symbiosis, are not well characterized. In this study, we present a novel yet objective method for quantifying hormogonia induction, addressing limitations of traditional qualitative approaches. We have developed a reporter strain of Nostoc punctiforme PCC 73102 capable of quantifying hormogonia induction in response to diverse biotic and abiotic stimuli. This reporter strain, generated via triparental mating conjugation transformation, contains the promoter sequence of prepilin pilA fused to a green fluorescent protein (GFP) and enables quantitative and high throughput monitoring of hormogonia induction using a microplate reader. Our innovative approach, using a cyanobacterial hormogonia reporter strain, allows high-throughput screening of the hormogonia-inducing effect of a wide array of environmental and plant signals. This method is expected to greatly advance our understanding of the genetic determinants underpinning plant-cyanobacteria symbioses.},
}

@article {pmid40357891,
year = {2025},
author = {Salem, MA and Jamil, M and Wang, JY and Berqdar, L and Liew, KX and Paramita, A and Ablazov, A and Balakrishna, A and Al-Babili, S},
title = {Disruption of the Karrikin Receptor DWARF 14 LIKE (D14L) Gene Leads to Distinct Effects on Root and Shoot Growth, and Reprogramming of Central Metabolism in Rice.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf201},
pmid = {40357891},
issn = {1460-2431},
abstract = {The rice (Oryza sativa L.) α/β hydrolase D14 LIKE (D14L), a paralog of the strigolactone receptor D14, is essential for the establishment of arbuscular mycorrhizal (AM) symbiosis and responses to karrikins, smoke-derived compounds that regulate several developmental processes. It is supposed that D14L is the receptor for a yet unidentified endogenous growth regulator. Herein, we determined the effects of disrupting the D14L on rice growth and metabolism. Our results revealed that the D14L loss of function altered rice architecture, leading to a significant increase in root growth and mesocotyl elongation, while hindering shoot growth, and a notable decrease in the number of tillers, especially under phosphate limiting conditions. Furthermore, d14l mutants exhibited significant reduction in the total grain yield. Metabolomics analysis revealed a notable shift of key metabolites, such as carbohydrates and amino acids involved in energy production and growth, from shoots to roots. This redistribution likely reflects an adaptive strategy to enhance nutrient acquisition and increase root biomass, albeit at the cost of shoot growth and productivity. Our findings highlight the pivotal role of D14L in regulating the root-to-shoot growth ratio and in coordinating the metabolism and allocation of resources across the rice plant.},
}

@article {pmid40357403,
year = {2025},
author = {Mejías, S and Jiménez, NE and Conca, C and Salgado, JC and Gerdtzen, ZP},
title = {Unveiling Wolbachia transcriptomic signature in the arboviral vector Aedes aegypti.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1538459},
pmid = {40357403},
issn = {2235-2988},
mesh = {Animals ; *Wolbachia/genetics/physiology ; *Aedes/microbiology/genetics/virology ; *Mosquito Vectors/microbiology/genetics/virology ; Symbiosis/genetics ; *Transcriptome ; Gene Expression Profiling ; Female ; },
abstract = {INTRODUCTION: The mosquito Aedes aegypti is the main vector of arboviral diseases such as dengue and imposes a global health burden. A promising control strategy is to infect A. aegypti populations with Wolbachia, a genus of intracellular bacteria capable of blocking arboviral infections. Enhancing and preserving the efficacy of this method will depend on a solid mechanistic knowledge of the A. aegypti-Wolbachia symbiosis. By identifying differences between Wolbachia-infected and uninfected A. aegypti, previous transcriptomic studies proposed a wide range of symbiotic interactions, but a systematic identification of consistent effects across datasets is still missing.

METHODS: To identify A. aegypti genes and functions consistently affected by Wolbachia, we performed differential expression and functional enrichment analysis on published transcriptomic datasets, followed by a meta-analysis of the obtained p-values using the maxP method. Six datasets were retrieved from Gene Expression Omnibus, Sequence Read Archive and ArrayExpress (last searched in July 2024, considering lack of replication as the exclusion criteria). After discarding one dataset from wAlbB-infected cell line due to poor mapping to the A. aegypti genome, the data comprised adult female A. aegypti heads, muscles, carcasses, midguts and bodies, and Wolbachia strains wMel and wMelPop.

RESULTS AND DISCUSSION: Meta-analysis revealed 10 and 21 consistently down- and upregulated host genes, some of which have escaped the focus of previous research, including the consistently downregulated exonuclease AAEL009650 which has a pro-dengue virus homolog in Drosophila. At the function level, we found consistent upregulation of electron transport chain (ETC), carbohydrate transport and serine-type peptidase activity and inhibition, and downregulation of DNA replication. ETC upregulation suggests an alternative mechanism for Wolbachia's induction of antiviral oxidative stress, previously attributed to dual- and NADPH-oxidases which here showed downregulation or no regulation. Through analysis of previously published datasets, this work identifies promising molecular and functional targets for future studies aimed at elucidating the most fundamental mechanisms of the A. aegypti-Wolbachia symbiosis.},
}

Animals
*Wolbachia/genetics/physiology
*Aedes/microbiology/genetics/virology
*Mosquito Vectors/microbiology/genetics/virology
Symbiosis/genetics
*Transcriptome
Gene Expression Profiling
Female

@article {pmid40356659,
year = {2025},
author = {Zheng, X and Liu, R and Li, K and Sun, J and Wang, K and Shao, Y and Hu, Z and Zhu, J and Pan, Z and Nakhla, G},
title = {Microalgae-bacteria symbiosis enhanced nitrogen removal from wastewater in an inversed fluidized bed bioreactor: performance and microflora.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1591974},
pmid = {40356659},
issn = {1664-302X},
abstract = {Conventional wastewater biological nitrogen removal (BNR) processes require a large amount of air and external organic carbon, causing a significant increase in operating costs and potential secondary pollution. Herein, this study investigated the nitrogen removal performance and the underlying mechanisms of a novel simultaneous nitrification and denitrification (SND) coupled with photoautotrophic assimilation system in an inversed fluidized bed bioreactor (IFBBR). Nitrogen removal was achieved through the synergistic interaction of microalgae and bacteria, with microalgae providing O2 for nitrification and microbial biomass decay supplying organic carbon for denitrification. The IFBBR was continuously operated for more than 240 days without aeration and external organic carbon, the total nitrogen (TN) removal efficiency reached over 95%. A novel C-N-O dynamic balance model was constructed, revealing that nitrification and denitrification were the primary pathways for nitrogen removal. The model further quantified the microbial contributions, showing that microalgae generated O2 at a rate of 81.82 mg/L·d, while microbial biomass decay released organic carbon at a rate of 148.66 mg/L·d. Microbial diversity analysis confirmed the majority presence of microalgae (Trebouxiophyceae), nitrifying bacteria (Gordonia and Nitrosomonas) and denitrifying bacteria (Ignavibacterium and Limnobacter). This study successfully achieved enhanced nitrogen removal without the need for aeration or external organic carbon. These advancements provide valuable insights into efficient wastewater nitrogen removal, offering significant benefits in terms of reduced energy consumption, lower operational costs, and decreased CO2 emissions.},
}

@article {pmid40355047,
year = {2025},
author = {Yu, J and Wang, D and Zhao, T and Yu, X and Liu, S and Wang, Y and Wang, K and Zhao, M and Chen, P and Wang, Y and Zhang, M},
title = {Potential Participants and Regulatory Factors in Ginsenoside Biosynthesis of Panax Ginseng C.A. Meyer: The Role of Endophytic Fungus PBF-08.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112553},
doi = {10.1016/j.plantsci.2025.112553},
pmid = {40355047},
issn = {1873-2259},
abstract = {Panax ginseng C.A. Meyer was recognized as a precious traditional Chinese medicine with a long history of application. It is widely used due to its high medicinal value. Ginsenosides were identified as a group of triterpenoid secondary metabolites in ginseng and were considered the main active ingredients of ginseng. Plant endophytes were recognized as microorganisms that resided within plant tissues, coexisting with the host plant for part or all of their life cycle and interacting with the external environment together. Ginseng endophytes, as symbiotic microorganisms with ginseng, possess various functions such as enhancing yield, increasing resistance, and improving quality, making them an important microbial resource for potential utilization. In this study, we screened and identified an endophytic fungus PBF-08, which has the ability to produce ginsenosides Rg2, Rg3, and Re. By optimizing its fermentation conditions using the response surface methodology, the total ginsenoside yield was significantly increased. Additionally, ginseng adventitious roots were treated with strain PBF-08 as an elicitor, which significantly increased the ginsenoside content by regulating the expression of key enzyme genes in the ginsenoside biosynthesis pathway under optimal treatment concentration and time. Widely targeted metabolomic analysis revealed that strain PBF-08 not only possesses a complete and active terpenoid biosynthesis pathway but also synthesizes various metabolites that influence plant growth and metabolism. In summary, the strain PBF-08 was found to have potential application value in exploring new methods for obtaining ginsenosides and in developing microbial elicitors for regulating ginsenoside biosynthesis.},
}

@article {pmid40351789,
year = {2025},
author = {Bourgeois, D and Orsini, G and Carrouel, F},
title = {Editorial: Exploring oral microbiota dysbiosis as a risk factor for oral and non-communicable diseases.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1611120},
pmid = {40351789},
issn = {2673-4842},
}

@article {pmid40349586,
year = {2025},
author = {Wang, X and Du, C and Li, Y and Liu, S and Zeng, X and Li, Y and Wang, S and Jia, Y},
title = {Metal pollution-induced alterations in soil fungal community structure and functional adaptations across regional scales.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138553},
doi = {10.1016/j.jhazmat.2025.138553},
pmid = {40349586},
issn = {1873-3336},
abstract = {Soil contamination with heavy metal(loid)s (HMs) threatens soil ecosystem health and function. However, how cross-regional HM contamination influences the structure and function of soil fungal communities remains understudied. We conducted a large-scale soil survey in southern China, using the Nemerow synthetic Pollution Index to assess contamination levels of seven metals (copper, lead, cadmium, arsenic, nickel, zinc and chromium). Soils were classified as low, medium, and high contamination (LC/MC/HC) to examine HM biogeographic patterns and their ecological impacts on soil fungi along the gradient. Cd was the most prevalent contaminant, followed by As in all the studied soils. The combined soil pollution significantly altered fungal community structure, with Cd and Pb identified as key drivers of structural and evenness changes, respectively. Fungal diversity and evenness declined with pollution, accompanied by reduced Staphylotrichum (-0.45 %) and Saitozyma (-1.5 %). Homogeneous selection dominated the assembly processes of soil fungal communities across all contamination levels (contributing 55.8-64.9 %). The most enriched characteristic species included Eurotiomycetes (LC), Sordariales (MC), and Coniochaeta (HC). Pollution-induced habitat heterogeneity enhanced the complexity and stability of fungal symbiotic networks, with 10.0 % more synergistic interactions in highly contaminated soils. The abundance of potential pathogenic fungi increased by 3.0-5.8 % in highly polluted soils compared to low- and moderately polluted soils, indicating possible negative implications for ecosystem health. Our findings provide novel and comprehensive insights into the ecological response of soil fungal communities to HM contamination.},
}

@article {pmid40349544,
year = {2025},
author = {Guo, X and Huang, L and Miao, H and Mi, L and Han, Z},
title = {Exploring carbon reduction pathways in the steel industry from the perspective of emerging technologies for achieving carbon neutrality.},
journal = {Journal of environmental management},
volume = {385},
number = {},
pages = {125768},
doi = {10.1016/j.jenvman.2025.125768},
pmid = {40349544},
issn = {1095-8630},
abstract = {The iron and steel industry (ISI) plays a pivotal role in global decarbonization efforts, yet achieving carbon neutrality remains a significant challenge due to the sector's high emissions and technological complexity. Strategically identifying emerging technologies is critical for aligning industrial transformation with climate goals, optimizing resource allocation, and mitigating transition risks in a rapidly evolving technological landscape. This study bridges this gap by developing a multi-source data analytical framework that integrates Topmine phrase mining, K-means clustering, and Text2vec similarity analysis. The framework enhances the identification of emerging technologies through a reverse verification mechanism, ensuring the robustness of clustering results. By systematically classifying technologies into hot, growing, mature, and weak-signal categories, this study uncovers key technological pathways shaping the future of ISI decarbonization. Additionally, topic phrase burst analysis is employed to forecast technology evolution trends, revealing key shifts such as multi-technology integration for synergistic effects, intelligent process optimization, and industrial symbiosis. These methodological advancements not only provide a replicable toolkit for strategic decision-making but also empower stakeholders to prioritize investments, foster cross-sector collaboration, and accelerate the ISI's transition to carbon neutrality. The findings offer a transformative roadmap for policymakers and enterprises to navigate technological uncertainties while balancing economic competitiveness and environmental imperatives.},
}

@article {pmid40348264,
year = {2025},
author = {Hu, Z and Li, Z and Xu, Y and He, F and Zhang, J and Li, T},
title = {MgFe-LDHs/Vallisneria natans combined system for simultaneous elimination of endogenous N and P pollution in eutrophic water: Performance, synergetic mechanism, and metagenomics analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121798},
doi = {10.1016/j.envres.2025.121798},
pmid = {40348264},
issn = {1096-0953},
abstract = {Eutrophication is the main factor for the degradation of lake ecosystems. More than exogenous input, endogenous N and P nutrients are responsible for it. Although the P passivation technology with functional materials is common for alleviating endogenous P pollution, will it have the same effect for endogenous N removal? In this study, a novel MgFe-LDHs/Vallisneria natans (V. natans) combined system was established for effective eliminating endogenous N and P simultaneously. During remediation periods, MgFe-LDHs/V. natans combined system with the most obvious improvement for overlying water quality that was reflected by DO, ORP, and SS, and TP, TN, and NH4[+]-N removal efficiency were up to 99%. In sediments, TP and TN removal rate was approximately 68% and 63%, where the reduction of Org-P and NH4[+]-N accounted for the majority of it, respectively. Under stimulation of MgFe-LDHs, NH4[+]-N assimilation in V. natans could be promoted through improving the metabolizing enzymes activity. In turn, V. natans contributed to Org-P mineralization by secreting organic acid, further facilitating IP enrichment on MgFe-LDHs. Additionally, owing to the synergism between V. natans allelopathy and MgFe-LDHs, the symbiotic relationship between microbial communities was much closer and more stable, the expression of functional genes that relate to denitrification, assimilatory nitrate reduction, phosphorylation and organophosphorus mineralization processes were up-regulated prominently. That is, microorganisms acted synergistically were important for endogenous N and P elimination performance. This study proposed a high-efficiency and environmentally friendly materials/plants combined remediation technology for eutrophication, especially those where with much high endogenous N and P loading.},
}

@article {pmid40347990,
year = {2025},
author = {Wang, Y and Ekblom, C and Kruangkum, T and Uribeondo, JD and Söderhäll, K and Söderhäll, I},
title = {Specific host factors determine resistance in a North American crayfish to the crayfish plague, Aphanomyces astaci.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110392},
doi = {10.1016/j.fsi.2025.110392},
pmid = {40347990},
issn = {1095-9947},
abstract = {The crayfish plague is caused by the oomycete Aphanomyces astaci with North American crayfish (for example Pacifastacus leniusculus and Procambarus clarkii) serving as carriers and vectors for this pathogen. This poses a constant threat to native crayfish in Europe, Asia, South America and Australia, which all are highly susceptible to this pathogen. In this study we now show how the symbiotic balance between the pathogen and its host are maintained at the molecular level. The host factors involved in this balance between the pathogen, A. astaci and the host, P. leniusculus, are one glycine-rich antimicrobial peptide (GRP) that is specifically active against A. astaci, but not to other microorganisms and two Kazal proteinase inhibitors (KPI2 and KPILA) inhibit secreted A. astaci proteases by binding to subtilisin enzymes from the pathogen. Accordingly, the expression of GRP, KPI2, KPILA, as well as proPO mRNAs increases following A. astaci infection. Silencing GRP, or KPI2 + KPILA mRNAs results in death of the crayfish from infection. Over time, this host-pathogen relationship has evolved to allow resistant crayfish to coexist with A. astaci in their cuticle for life, provided critical components remain unaltered by environmental changes or other pathogens. It is unclear whether a similar relationship could develop between currently susceptible crayfish and A. astaci.},
}

@article {pmid40346478,
year = {2025},
author = {de Oliveira, BR and Zuffo, AM and Dos Santos Silva, FC and Steiner, F and AlGarawi, AM and Okla, MK and Nhs, M and Alhaj Hamoud, Y and Josko, I and Sheteiwy, MS and Alyafei, MS and Sulieman, S},
title = {Random forest algorithms: a tool to identify the impact of arbuscular mycorrhizal fungi inoculation, seed maturation stage and geographic diversity of Pimpinella anisum L. accessions on the physicochemical composition of seeds.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {608},
pmid = {40346478},
issn = {1471-2229},
support = {RSPD2024R931//King Saud University/ ; RSPD2024R931//King Saud University/ ; },
mesh = {*Mycorrhizae/physiology ; *Seeds/growth & development/microbiology/chemistry ; *Algorithms ; *Pimpinella/microbiology/growth & development/chemistry ; Symbiosis ; Principal Component Analysis ; Random Forest ; },
abstract = {BACKGROUND: A study using random forest (RF) algorithms and principal component analysis (PCA) was proposed to identify the effects of arbuscular mycorrhizal fungal inoculation, the seed maturation stage and the geographic diversity of Pimpinella anisum L. accessions on the physicochemical composition of seeds. Seeds of six anise varieties from North African and Middle Eastern accessions were inoculated or not inoculated with AMF (an arbuscular mycorrhizal fungus) and then grown under controlled conditions. Seeds were harvested at three different maturity stages: mature seeds (157 d after sowing), premature seeds (147 d after sowing), and immature seeds (137 d after sowing). Forty-nine variables related to physical properties, total nutrients, metabolic compounds, essential oils, and biological activity were measured in P. anisum seeds.

RESULTS: The RF algorithm allows the differentiation of P. anisum varieties inoculated with AMF from different countries in North Africa and the Middle East. This evidence proves that the geographic origin of P. anisum seeds significantly influences the efficiency of the symbiotic association between anise roots and AMF. In turn, no significant effects of the seed maturation stage on the symbiotic interaction of plants with mycorrhizae were observed. The chemical compounds related to the biological activity of seeds are not influenced by AMF, followed by chemical compounds related to metabolism, total nutrients, and oil components.

CONCLUSIONS: The performance of classification models using RF is driven primarily by independent variables related to the chemical composition of anise seeds, overshadowing the effects of geographic diversity and the seed maturation stage. Among the chemical constituents of the seed, the variables belonging to the biological activity category best contain information (patterns) on the impacts of AMF inoculation.},
}

*Mycorrhizae/physiology
*Seeds/growth & development/microbiology/chemistry
*Algorithms
*Pimpinella/microbiology/growth & development/chemistry
Symbiosis
Principal Component Analysis
Random Forest

@article {pmid40345999,
year = {2025},
author = {Bačić, A and Abboud, KY and Zhang, Y and Rajilić-Stojanović, M},
title = {Yarrow (Achillea millefolium) Extract Modulates the Gut Microbiota Composition and Activity in the TIM-2 In Vitro Model of the Colon.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70074},
doi = {10.1002/mnfr.70074},
pmid = {40345999},
issn = {1613-4133},
support = {451-03-68/2022-14/200135//Science and Technological Development of the Republic of Serbia/ ; 101060130//Horizon Europe 2021-2027 research and innovation program, TwinPrebioEnz/ ; },
abstract = {Phenolic compounds, abundantly found in medicinal herbs, may promote health by modulating the gut microbiota. Yarrow is a traditional remedy for digestive and non-gastrointestinal diseases with unexplored interaction with gut microbes. This study aimed to evaluate the effects of yarrow extract and a phenolic mixture comprising apigenin, caffeic, and chlorogenic acids on the gut microbiota using the TIM-2 in vitro system. The TIM-2 units were inoculated with fecal samples from healthy individuals and supplemented with test substrates for 72 h. Microbiota composition was assessed by V3-V4 16S rRNA gene sequencing, while organic acid production was evaluated by GC-MS. The yarrow extract stimulated probiotic bacteria Lactiplantibacillus, and other abundant and symbiotic gut inhabitants, including Eggerthellaceae, Christensenellaceae, Butyricicoccaceae, and the Eubacterium coprostanoligenes group. The phenolic mixture exerted milder effects on gut microbiota by enhancing the growth of Eggerthellaceae and Collinsella. Looking at the microbial activity, the production of SCFAs, specifically acetic and propionic acids, was increased in the yarrow group. The obtained results highlight the importance of yarrow phenolics in maintaining microbiota balance. The yarrow extract and specific phenolics may modulate the gut microbiota by promoting the growth of SCFA producers and stimulating SCFA synthesis.},
}

@article {pmid40343785,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40343785},
issn = {1472-765X},
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

@article {pmid40342598,
year = {2025},
author = {Meng, XX and Jia, X and Zhao, YH},
title = {Effects of arbuscular mycorrhizal fungi on flavonoid content in Astragali Radix cultivated in cadmium-contaminated soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1576236},
pmid = {40342598},
issn = {1664-302X},
abstract = {INTRODUCTION: As bioactive components in Astragali Radix (AR), flavonoids can promote hematopoiesis and have hypolipidemic properties, among others, and they are easily affected by environmental factors. Arbuscular mycorrhizal fungi (AMF) can influence flavonoid synthesis in plants exposed to heavy metals by expanding the root absorption area to establish a reciprocal symbiotic relationship with most plants.

METHODS: We investigated the effects of Funneliformis mosseae and time on the total flavonoids and key monomers (calycosin, calycosin-7-glucoside, formononetin, and ononin) in AR exposed to cadmium (Cd) using a pot experiment. The treatments consisted of non-inoculation and F. mosseae inoculation. A two-way analysis of variance and Duncan's test were conducted.

RESULTS: Shoot total flavonoids decreased (p < 0.05) at 60 (20.5%) and 90 d (18.3%), while formononetin decreased (83.4%) by 120 d; conversely, calycosin-7-glucoside increased (p < 0.05) with inoculation, although calycosin-7-glucoside decreased (p < 0.05) over time from 60 to 120 d regardless of inoculation. Shoot calycosin increased (p < 0.05) over time regardless of inoculation. Root total flavonoids decreased (p < 0.05) by 15.2% at 60 d, then increased (p < 0.05) by 23.5% at 90 d, along with increases in formononetin (117.1%) and ononin (59.6%) at 60 d, and calycosin-7-glucoside (21.2%) at 120 d, which increased (p < 0.05) under inoculation. The colonization rate, along with shoot Cd, C, P, H, and C/N ratio, significantly affected shoot flavonoids, while Cd accounted for 90.0% of flavonoid variation, which may be associated with its impact on flavonoid synthase. The variation in root flavonoids was significantly influenced by root S, biomass, and N, suggesting that AMF regulation may vary between AR organs. Calycosin-7-glucoside was significantly affected by phenylalanine ammonia-lyase (a key gene in flavonoid synthesis). Overall, F. mosseae led to significant increases in shoot total flavonoids and calycosin-7-glucoside. The total flavonoids were higher in shoots than in roots, indicating that annual AR shoots exposed to Cd may be utilized for medicinal purposes under inoculation.

DISCUSSION: These results provide insights into the enhancement of AMF on the quality of medicinal plants grown in Cd-contaminated soils, and the long-term effects of AMF on flavonoids at varying Cd levels should be further investigated.},
}

@article {pmid40339063,
year = {2025},
author = {Zavala-Mazariegos, FJ and Cruz-Esteban, S and Álvarez-Solís, JD and Rojas, JC},
title = {Mycorrhizal fungus colonization on maize seedlings diminishes oviposition of fall armyworm females and affect larval performance.},
journal = {Environmental entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ee/nvaf045},
pmid = {40339063},
issn = {1938-2936},
abstract = {Arbuscular mycorrhizal fungi are key components of the soil microbiota and are characterized by their symbiosis with terrestrial plants. In addition to providing nutrients to plants during symbiosis, arbuscular mycorrhizal fungi can enhance plant defenses against herbivorous insects and pathogens, including induced systemic resistance. Previous studies have demonstrated that Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) larvae perform better in maize plants colonized by arbuscular mycorrhizal fungi, which generally exhibit greater growth and higher nitrogen and phosphorus contents. However, these studies were limited to a small number of maize varieties. Additionally, prior research has not considered the host preference of S. frugiperda females for noncolonized versus arbuscular mycorrhizal fungi-colonized maize plants, although female choice can significantly influence progeny performance. In this study, we evaluated the effects of Rhizophagus irregularis (Blaszk, Wubet, Renker, & Buscot) C. Walker & A. Schüßler (Glomerales: Glomeraceae) inoculation on 4 maize inbred lines (CML 124, CML 343, CML 122, and CML 126) susceptible to S. frugiperda on female oviposition preference and larval performance of S. frugiperda. Overall, females preferred ovipositing on uncolonized seedlings to arbuscular mycorrhizal fungi-colonized seedlings, independent of the inbred lines. Larval performance was affected by inbred lines and arbuscular mycorrhizal fungi colonization. Larvae feeding on noncolonized maize seedlings exhibited significantly higher weights than those feeding on arbuscular mycorrhizal fungi-colonized seedlings. Among the inbred lines, larvae fed CML 122 performed better than those fed CML 126 and CML 343 seedlings. The weight of the larvae fed on CML 124 seedlings was similar to that of the larvae fed on CML 122, CML 126, and CML 343 seedlings.},
}

@article {pmid40338463,
year = {2025},
author = {Yang, G and Li, M and Zhang, J and Zhou, J and Cheah, WY and Abdullah, R and Ling, TC},
title = {Evaluation of cultivation conditions in hydrogel systems to enhance Chlorella vulgaris growth.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40338463},
issn = {1618-1905},
support = {MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; MG017-2022//Universiti Malaya/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; Geran Galakan Penyelidik Muda [GGPM-2022-048 & GGPM-2022-056)], Ganjaran Penerbitan [K024760]//Universiti Kebangsaan Malaysia/ ; },
abstract = {Microalgae have gained significant attention as sustainable alternatives to traditional agriculture and energy resources. The cultivation efficiency of microalgae within hydrogel systems presents a promising avenue for spatially efficient bio-production. However, the optimum cultivation conditions of hydrogel cultivation systems have not been elucidated. This study focused on evaluating the hydrogel-based cultivation of Chlorella vulgaris in symbiosis with Bacillus Strain Salmah Ismail (SI) 139SI. It investigated the impact of hydrogel concentration, pH, light exposure, and system thickness on the growth and chlorophyll production of the algae. Our findings highlighted that, in coculture, a 7% (w/v) hydrogel concentration, pH of 7.4, a 12-h light/dark cycle at a hydrogel concentration of 7% but continuous light exposure under 5% hydrogel concentration, and a system thickness of 10 mm have provided the most favorable environmental conditions for the proliferation and chlorophyll production of C. vulgaris. These conditions significantly enhanced the biomass yields, suggesting that tailored hydrogel environments can substantially improve microalgae productivity.},
}

@article {pmid40338334,
year = {2025},
author = {Diao, F and Liu, K and Wu, W and Xu, J},
title = {Leaf transcriptomic responses to arbuscular mycorrhizal symbioses exerting growth depressions in tomato.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {139},
pmid = {40338334},
issn = {1432-072X},
support = {2021BQ132//Program of Doctoral Research Foundation of Shanxi Agricultural University/ ; 2022ZDYF115//Shanxi Provincial Key Research and Development Project/ ; 2021YFD1901105//National Key Research and Development Program of China/ ; },
mesh = {*Mycorrhizae/physiology ; *Solanum lycopersicum/microbiology/growth & development/genetics/metabolism ; *Symbiosis ; *Transcriptome ; *Plant Leaves/microbiology/genetics/growth & development/metabolism ; *Glomeromycota/physiology ; Plant Roots/microbiology/growth & development ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Seedlings/microbiology/growth & development ; Carbon/metabolism ; Fungi ; },
abstract = {Arbuscular mycorrhizal (AM) fungi play important roles in sustainable agriculture, given that they provide multiple benefits for numerous crops. Conversely, negative plant growth effects induced by AM fungi are also occasionally observed. However, little information is available regarding the responses of symbiosis. In this study, compared with an absence of AM fungus inoculation, tomato seedlings inoculated with Funneliformis mosseae or Rhizophagus intraradices were characterized by reduced shoot and root growth. The two AM fungi decreased the carbon contents and the carbon-nitrogen ratios in shoots. To gain further insights into the underlying mechanisms, transcriptomic analyses were performed in the study. A total of 190 and 870 differentially expressed genes (DEGs) were identified in the F. mosseae vs. control and R. intraradices vs. control comparisons, respectively. KEGG enrichment analysis of the former 190 DEGs revealed significant enrichment of the "Protein processing in endoplasmic reticulum," "Flavonoid biosynthesis," "Flavone and flavonol biosynthesis," and "Stilbenoid, diarylheptanoid, and gingerol biosynthesis" pathways, whereas "DNA replication," "Photosynthesis - antenna proteins," "Cutin, suberine, and wax biosynthesis," "Protein processing in endoplasmic reticulum," and "Glycerophospholipid metabolism" were identified as pathways significantly enriched with the latter 870 DEGs. GO functional analysis revealed that among both groups of DEGs, large numbers of genes were assigned the "Response to stimulus" term. Moreover, many of the enriched terms were associated with stimulus and stress response processes, including response to salt stress, heat, and reactive oxygen species. Therefore, the findings indicated that AM fungi may trigger defense-related responses in hosts, even though the symbioses performed growth depressions. These findings will contribute to advancing our current understanding of AM fungi.},
}

*Mycorrhizae/physiology
*Solanum lycopersicum/microbiology/growth & development/genetics/metabolism
*Symbiosis
*Transcriptome
*Plant Leaves/microbiology/genetics/growth & development/metabolism
*Glomeromycota/physiology
Plant Roots/microbiology/growth & development
Gene Expression Regulation, Plant
Gene Expression Profiling
Plant Proteins/genetics/metabolism
Seedlings/microbiology/growth & development
Carbon/metabolism
Fungi

@article {pmid40338317,
year = {2025},
author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A},
title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {42},
pmid = {40338317},
issn = {1432-184X},
support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; },
mesh = {*Endophytes/genetics/isolation & purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation & purification/physiology ; *Ascomycota/genetics/isolation & purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; },
abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.},
}

*Endophytes/genetics/isolation & purification/physiology
*In Situ Hybridization, Fluorescence/methods
Plant Roots/microbiology
*Mycorrhizae/genetics/isolation & purification/physiology
*Ascomycota/genetics/isolation & purification/physiology
Symbiosis
Italy
Polymerase Chain Reaction
Hyphae/genetics

@article {pmid40337257,
year = {2025},
author = {Zemeitat, DS and Coquilleau, M and Pierce, NE and Elgar, MA},
title = {Ant responses in a lycaenid-ant symbiosis are not facilitated by cuticular compounds alone.},
journal = {Royal Society open science},
volume = {12},
number = {5},
pages = {241320},
pmid = {40337257},
issn = {2054-5703},
abstract = {Initiating partnerships in protective symbioses can be asymmetrical if there is a risk of attack from their symbionts. Myrmecophiles may encounter chemically mediated recognition systems that allow the host ants to distinguish nestmates from natural enemies, including non-nestmate conspecifics. The immature stages of the lycaenid butterfly Jalmenus evagoras form an obligate symbiosis with workers of Iridomyrmex mayri that protect them against natural enemies. However, the first instar larvae cannot anticipate this colony-specific chemical recognition system, since they are unlikely to encounter workers from the same colony that tended their mother. We show experimentally that workers of I. mayri can use chemical signals alone to distinguish between conspecifics and the larvae of J. evagoras; between nestmate and non-nestmate conspecifics and between larvae tended by nestmate and non-nestmate conspecifics. Nevertheless, we also show experimentally that while workers paid more attention to fourth than second instar larvae, they did not respond more aggressively to larvae that had been tended by non-nestmate versus nestmate workers. These data suggest that workers pay attention to other signals, perhaps via tactile, visual or vibratory sensory modalities, thereby allowing the butterfly myrmecophiles to mitigate the risks associated with the chemically mediated colony-specific recognition systems of their ant hosts.},
}

@article {pmid40336531,
year = {2025},
author = {Ma, P and Li, Y and Hao, J and Lu, H and He, Y and Wei, L and Ai, L and Wang, S},
title = {Co-Culture of Lactobacillus bulgaricus With Streptococcus thermophilus and Bifidobacterium Impact the Metabolism and Flavor of Fermented Milk.},
journal = {Food science & nutrition},
volume = {13},
number = {5},
pages = {e70182},
pmid = {40336531},
issn = {2048-7177},
abstract = {Incorporating Bifidobacterium into fermented milk alters the balance between Lactobacillus bulgaricus and Streptococcus thermophilus. We investigated the bacterial interaction and metabolism post-fermentation and during 21-day storage. Utilizing non-targeted metabolomics and electronic nose technology, we assessed impacts on product quality and flavor. Bifidobacterium significantly increased the viability of the other two species, with AI-2 levels rising in the mixed culture. Metabonomic analysis revealed distinct metabolic profiles, with Bifidobacterium-fermented milk showing enriched key metabolites. Volatile compounds like ketones, aldehydes, esters, alcohols, and acids were identified, with 2-heptanone and 2-pentanone as initial discriminators and 2-pentanone and acetaldehyde as key flavor compounds after storage. This study advances understanding of symbiotic interactions and metabolite profiles in fermented dairy ecosystems.},
}

@article {pmid40335917,
year = {2025},
author = {Lan, M and Gao, K and Qin, Z and Li, Z and Meng, R and Wei, L and Chen, B and Yu, X and Xu, L and Wang, Y and Yu, K},
title = {Coral microbiome in estuary coral community of Pearl River Estuary: insights into variation in coral holobiont adaptability to low-salinity conditions.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {278},
pmid = {40335917},
issn = {1471-2180},
support = {42206157//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; GXLSCRSCS2022103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; 2022GXNSFBA035449//Natural Science Foundation of Guangxi Province/ ; PM-zx703-202004-143//Central Public-Interest Scientific Institution Basal Research Fund/ ; },
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Estuaries ; *Microbiota ; Salinity ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Rivers ; Biodiversity ; Phylogeny ; Adaptation, Physiological ; RNA, Ribosomal, 16S/genetics ; Dinoflagellida/genetics/classification/physiology ; Ecosystem ; China ; },
abstract = {BACKGROUND: Low salinity is a crucial environmental stressor that affects estuarine coral ecosystems considerably. However, few studies have focused on the effects of low-salinity conditions on coral-associated microorganisms and the adaptability of coral holobionts.

METHODS: We explored the community structure of coral symbiotic Symbiodiniaceae and associated bacteria in low-salinity conditions using samples of six coral species from the Pearl River Estuary and analyzed the adaptability of coral holobionts in estuaries.

RESULTS: The symbiotic Symbiodiniaceae of all six studied coral species were dominated by Cladocopium, but, the Symbiodiniaceae subclades differed among these coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of symbiotic Symbiodiniaceae but low Symbiodiniaceae density, with different adaptability to low-salinity stress in the Pearl River Estuary. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by associating with specific Symbiodiniaceae subclades and with high Symbiodiniaceae density under low-salinity stress. The microbiome associated with the coral species were dominated by Proteobacteria, Chloroflexi, and Bacteroidetes; however, its diversity and composition varied among coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of associated bacteria, with different adaptability owing to low-salinity stress. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by having minority bacterial dominance under low-salinity stress.

CONCLUSIONS: High Symbiodiniaceae density and high bacterial diversity may be conducive to increase the tolerance of coral holobiont to low-salinity environments. Different coral species have distinct ways of adapting to low-salinity stress, and this difference is mainly through the dynamic regulation of the coral microbiome by corals.},
}

Animals
*Anthozoa/microbiology/physiology
Estuaries
*Microbiota
Salinity
*Bacteria/classification/genetics/isolation & purification
Symbiosis
Rivers
Biodiversity
Phylogeny
Adaptation, Physiological
RNA, Ribosomal, 16S/genetics
Dinoflagellida/genetics/classification/physiology
Ecosystem
China