@article {pmid40934553,
year = {2025},
author = {Zonneveld, KL and Bustos-Diaz, ED and Francisco, BG and Angelica, CJ},
title = {The cycad coralloid root: is there evidence for plant-microbe coevolution?.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102660},
doi = {10.1016/j.mib.2025.102660},
pmid = {40934553},
issn = {1879-0364},
abstract = {Cycads are survivors, ancient plants originating in the Carboniferous. We hypothesize that cycad resilience and recent diversification could be partially explained by their specialized coral-like (coralloid) roots and their microbiome and that these symbiotic partners are co-evolving. The coralloid root is unique in gymnosperms and rare in vascular plants. Coralloid roots and their associated microbes have been studied since the late 19th century, but a deeper understanding of their taxonomy and function has taken place only recently. And yet, we are at the 'tip of the root' as there are many open questions regarding this specialized organ and its evolutionary history. This review provides an overview of cycad coralloid roots and their microbiome, the technical limitations of their study to date, and the exciting questions that remain to be answered.},
}

@article {pmid40934431,
year = {2025},
author = {Wang, Y and Liu, M},
title = {Relational vulnerability and technological mediation: The ethics of intelligent eldercare.},
journal = {Nursing ethics},
volume = {},
number = {},
pages = {9697330251374394},
doi = {10.1177/09697330251374394},
pmid = {40934431},
issn = {1477-0989},
abstract = {In current China, the 9073 elderly care system is accelerating the process of intelligentization. The fundamental tension between conventional filial piety ethics and technological rationality is evident in the numerous ethical debates triggered by intelligent older people's care services, despite their convenience. This study proposes an analytical paradigm called relational vulnerability, which creatively combines the philosophy of technology with Confucian relational ethics. Through the use of intricate mechanisms, this framework seeks to shed light on how technological mediation alters intergenerational ethics. According to research, intelligent services that improve physical care for older people while weakening emotional ties have a paradoxical effect that creates new kinds of alienation, such as the measurement of filial duty and the breakdown of ritual-embodied behaviors. By incorporating cultural calibration into the development of human-machine symbiosis, this study addresses this issue by proposing the design concepts of "differential regulation" and "embodiment retention." This counteracts the interpretive shortcomings of the Western autonomy-based ethical paradigm in the context of Chinese older people care, creating new avenues for the application of Confucian bioethics in the age of technology and offering fresh perspectives on moral dilemmas in intelligent older people care.},
}

@article {pmid40931017,
year = {2025},
author = {Montoya, QV and Gerardo, NM and Martiarena, MJS and Solís-Lemus, C and Kriebel, R and Schultz, TR and Sosa-Calvo, J and Rodrigues, A},
title = {Digging into the evolutionary history of the fungus-growing-ant symbiont, Escovopsis (Hypocreaceae).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1340},
pmid = {40931017},
issn = {2399-3642},
support = {305269/2018-6//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; },
mesh = {Animals ; *Symbiosis ; *Ants/microbiology/physiology ; *Hypocreales/physiology/genetics/classification ; *Biological Evolution ; Phylogeny ; },
abstract = {Symbiotic relationships shape the evolution of organisms. Fungi in the genus Escovopsis share an evolutionary history with the fungus-growing "attine" ant system and are only found in association with these social insects. Despite this close relationship, there are key aspects of Escovopsis evolution that remain poorly understood. To gain further insight into the evolutionary history of these unique fungi, we delve deeper into Escovopsis' origin and distribution, considering the largest sampling, so far, across the Americas. Furthermore, we investigate Escovopsis' trait evolution, and relationship with attine ants. We demonstrate that, while the genus originated approximately 56.9 Mya, it only became associated with 'higher attine' ants in the last 38 My. Our results, however, indicate that it is likely that the ancestor of Escovopsis lived in symbiosis with early-diverging fungus-growing ants. Since then, the fungi have evolved morphological and physiological adaptations that have increased their reproductive efficiency, possibly to overcome barriers mounted by the ants and their other associated microbes. Taken together, these results provide new clues as to how Escovopsis has evolved within the context of this complex symbiosis and shed light on the evolutionary history of the fungus-growing ant system.},
}

Animals
*Symbiosis
*Ants/microbiology/physiology
*Hypocreales/physiology/genetics/classification
*Biological Evolution
Phylogeny

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40928961,
year = {2025},
author = {Huang, X and Li, C and Zhang, K and Li, K and Xie, J and Quan, M and Sun, Y and Hu, Y and Xia, L and Hu, S},
title = {Engineering and Functional Expression of the Type III Secretion System in Xenorhabdus: Enhancing Insecticidal Efficacy and Expanding T3SE Libraries.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08269},
pmid = {40928961},
issn = {1520-5118},
abstract = {Entomopathogenic nematode symbiotic bacteria (EPNB) enhance nematode insecticidal capacity through symbiosis. This study cloned the complete 32-kb type III secretion system (T3SS) gene cluster from Photorhabdus luminescens TT01 using Red/ET recombineering and functionally expressed it in T3SS-deficient Xenorhabdus stockiae HN_xs01. Heterologous T3SS expression significantly enhanced HN_xs01 adhesion and invasion capabilities in CF-203 cells. In Helicoverpa armigera models, the engineered strain induced severe intestinal damage by suppressing antimicrobial peptide expression and demonstrated improved colonization and biocontrol efficacy (LC50 decreased by 3.7-fold). Crucially, the TT01 derived T3SS mediated delivery of XopA─a novel effector exhibiting YopJ-family homology and characteristic T3SS effector features─into host cells. These findings establish the synthetic biology-driven potential of T3SS and its effectors for biological control applications while providing a mechanistic framework for future research.},
}

@article {pmid40928749,
year = {2025},
author = {Fox, PT},
title = {Thirty years of SPM-BrainMap synergy: making and mining coordinate-based literature.},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
volume = {35},
number = {8},
pages = {},
doi = {10.1093/cercor/bhaf240},
pmid = {40928749},
issn = {1460-2199},
support = {AG082661//United States National Institutes of Health/ ; AG066456//United States National Institutes of Health/ ; AG076581//United States National Institutes of Health/ ; MH074457//United States National Institutes of Health/ ; },
mesh = {Humans ; *Brain/physiology/diagnostic imaging ; *Brain Mapping/methods/history ; Magnetic Resonance Imaging/methods ; *Data Mining ; Databases, Factual ; },
abstract = {Statistical Parametric Mapping (SPM) adheres to rigorous methodological standards, including: spatial normalization, inter-subject averaging, voxel-wise contrasts, and coordinate reporting. This rigor ensures that a thematically diverse literature is amenable to meta-analysis. BrainMap is a community database (www.brainmap.org; www.portal.brainmap.org) launched contemporaneously with SPM with the goal of efficiently sharing the results and methods of the literature compliant with SPM standards. The SPM-BrainMap symbiosis has motivated the development of coordinate-based meta-analytic methods and a substantial literature of secondary analyses. Collectively this corpus constitutes system-level probabilistic maps and models of the human brain, which details its functional organization, network architecture, and alterations by disease.},
}

Humans
*Brain/physiology/diagnostic imaging
*Brain Mapping/methods/history
Magnetic Resonance Imaging/methods
*Data Mining
Databases, Factual

@article {pmid40928528,
year = {2025},
author = {Zhang, X and Chen, L and Li, X and Zhang, L and Deveau, A and Martin, F and Zhang, X},
title = {Ectomycorrhizal symbiosis with Tuber spp. Enhances host performances in Pinus and Carya and induces host-specific patterns in defense-related regulation in the leaf transcriptomes.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {53},
pmid = {40928528},
issn = {1432-1890},
support = {2021YFYZ0026, 2024YFHZ0165//Science and Technology Support Project in Sichuan Province/ ; SCCXTD-2024-07//Sichuan Mushroom Innovation Team/ ; },
mesh = {*Mycorrhizae/physiology ; *Symbiosis ; *Pinus/microbiology/genetics/physiology/growth & development ; *Plant Leaves/microbiology/genetics/metabolism ; *Transcriptome ; *Plant Tubers/microbiology ; *Ascomycota/physiology ; Gene Expression Regulation, Plant ; },
abstract = {Ectomycorrhizal fungi (EMF) colonize roots to establish symbiotic associations with plants. Sporocarps of the EMF Tuber spp. are considered as a delicacy in numerous countries and is a kind of EMF of great economic and social importance. Elucidating host responses to Tuber colonization would facilitate the exploration of symbiotic interactions and contribute to truffle cultivation. Tuber indicum and T. panzhihuanense, two primary commercial truffle species in China, were selected to colonize Pinus armandii and Carya illinoinensis in a two-and-a-half-year symbiosis experiment. Host performances, including growth, nutrient uptake, and physiological characteristics, were dynamically monitored. The molecular response of host leaf to Tuber symbiosis was further analyzed using RNA-seq. Tuber indicum and T. panzhihuanense exhibited superior colonization of P. armandii compared to that of C. illinoinensis. Both Tuber species enhanced the performance of the two hosts by increasing their height, stem circumference, and biomass. Phosphorus levels and activities of peroxidase and catalase in hosts were observed to increase during Tuber symbiosis. The results confirmed that Tuber colonization led to significant alterations in leaf transcriptomic profiles of the two trees. Tuber indicum and T. panzhihuanense both elicited defense-related regulation in host leaves, such as secondary metabolism, cell wall biogenesis, plant hormone signal transduction, and plant-pathogen interaction, with distinct patterns in P. armandii and C. illinoinensis. Our study provides an evaluation of host performance during truffle symbiosis and highlights the diverse patterns of Tuber-induced systematic defense regulation in hosts, offering insights into the specific symbiotic traits of Tuber-host pairs.},
}

*Mycorrhizae/physiology
*Symbiosis
*Pinus/microbiology/genetics/physiology/growth & development
*Plant Leaves/microbiology/genetics/metabolism
*Transcriptome
*Plant Tubers/microbiology
*Ascomycota/physiology
Gene Expression Regulation, Plant

@article {pmid40927988,
year = {2025},
author = {Veresoglou, SD},
title = {Mycorrhizal ecology: In the land of the one-eyed king.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf399},
pmid = {40927988},
issn = {1460-2431},
abstract = {Unlike most of the other disciplines in microbial ecology, a substantial fraction of the theory on mycorrhizal ecology originates from times when assaying microbes was laborious and inefficient. Most of those hypotheses target, as a result, the plant partner of the symbiosis, or at best treat the two mycorrhizal partners as a unified organism, a holobiont. I here address the legacy of this era of mycorrhizal ecology, as a means of systematizing our understanding of the discipline, but also identifying gaps of knowledge. First, I pair and review hypotheses that align with the holobiont concept with complementary hypotheses that explicitly consider the fitness of the mycorrhizal fungus. Second, I generate a hierarchy of hypotheses in mycorrhizal ecology to showcase the high potential for classifying theory that the distinction between hypotheses considering mycorrhiza as either a holobiont or an association of two individual partners maintains. Third, I identify settings that might dictate when to better abstract mycorrhizas into holobionts and when to consider all their partners individually to foster research progress. I conclude the review with suggestions on how to further unify expectations in mycorrhizal ecology.},
}

@article {pmid40927683,
year = {2025},
author = {Boyno, G and Danesh, YR and Çevik, R and Teniz, N and Demir, S and Calayır, O and Farda, B and Mignini, A and Mitra, D and Pellegrini, M and Porcel, R and Mulet, JM},
title = {Plant-fungus synergy against soil salinity: The cellular and molecular role of arbuscular mycorrhizal fungi.},
journal = {iScience},
volume = {28},
number = {9},
pages = {113384},
pmid = {40927683},
issn = {2589-0042},
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in disease control by establishing symbiotic relationships with plant roots. AMF improve salinity tolerance in plants by regulating the Na[+]/K[+] ratio through selective ion transport and mediate osmotic regulation by inducing the accumulation of osmotic-compatible solutes such as glycine betaine and proline to enable plant cells to maintain water content and the metabolic balance. AMF can also activate antioxidant defense responses by stimulating enzymes that protect plant cells from harmful oxidation and pathological infections. Plant salinity tolerance induced by AMF depends on abscisic acid (ABA)-dependent signaling mechanisms, calcium-calmodulin-dependent pathways, and reactive oxygen species (ROS)-modulated mitogen-activated protein kinase (MAPK) cascades. Therefore, future research should focus on optimizing the production and field efficacy of AMF-based inoculants, including their combined use with microbial biostimulants, to support the implementation of sustainable agricultural practices.},
}

@article {pmid40926683,
year = {2025},
author = {Guo, G and Zhao, C and Xu, W and Lu, B and Zhao, Y and Wang, Z},
title = {Treatment of Aquaculture Wastewater by Utilizing Single and Symbiotic Systems of Microalgae-Based Technology and Strigolactone Induction.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {9},
pages = {e70174},
doi = {10.1002/wer.70174},
pmid = {40926683},
issn = {1554-7531},
support = {212102110105//Henan Science and Technology Research Project of Research and utilization of key microorganisms for nitrogen transformation during composting of pond sediment/ ; HARS-22-16-Z1//Special Fund for Henan Agriculture Research System/ ; 31971514//National Natural Science Foundation of China/ ; 31670511//National Natural Science Foundation of China/ ; 2023ss04//Science and Technology Program of Suzhou/ ; },
mesh = {*Microalgae/physiology/metabolism ; *Aquaculture ; *Wastewater/chemistry ; *Lactones/metabolism ; Symbiosis ; *Waste Disposal, Fluid/methods ; *Heterocyclic Compounds, 3-Ring/metabolism ; *Chlorella vulgaris/metabolism ; },
abstract = {This study investigated the efficacy of two microalgae treatment systems (Chlorella vulgaris monoculture and a Chlorella vulgaris-S395-2-Clonostachys rosea symbiotic system) in treating aquaculture wastewater, under varying concentrations of synthetic strigolactone analog (GR24). By exposing the systems to four GR24 doses (0, 10[-11], 10[-9], and 10[-7] M), we examined the impact on biomass growth, photosynthesis, and wastewater treatment. Elevated GR24 concentrations bolstered metabolism and photosynthesis in the systems, fostering rapid symbiont growth and enhanced treatment efficiency. Notably, the coculture system outperformed the monoculture in terms of photosynthetic rate, daily biomass accumulation, and nutrient reduction in aquaculture wastewater (p < 0.05). Optimally, at 10[-9] M GR24, the symbiotic system achieved remarkable average removal rates of COD (78.54 ± 6.11%), TN (81.69 ± 7.02%), and TP (82.67 ± 7.58%) from aquaculture wastewater. Additionally, a comparative analysis revealed the system's exceptional capacity to reduce oxytetracycline hydrochloride (OTC) levels, achieving a notable 98.72% removal rate. The outcomes significantly advance bioenhancement approaches and inform the design of efficient algal-bacterial-fungal symbiotic processes for treating antibiotic-contaminated wastewater.},
}

*Microalgae/physiology/metabolism
*Aquaculture
*Wastewater/chemistry
*Lactones/metabolism
Symbiosis
*Waste Disposal, Fluid/methods
*Heterocyclic Compounds, 3-Ring/metabolism
*Chlorella vulgaris/metabolism

@article {pmid40926201,
year = {2025},
author = {Bakrani, Z and Ehsanzadeh, P},
title = {Mycorrhizal inoculation mitigates drought stress in borage (Borago officinalis L.): Evidence from biochemical, physiological, and growth responses.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1198},
pmid = {40926201},
issn = {1471-2229},
}

@article {pmid40925330,
year = {2025},
author = {Udvardi, M and Mens, C},
title = {Symbiosis: A SWEET deal for nodules.},
journal = {Current biology : CB},
volume = {35},
number = {17},
pages = {R830-R832},
doi = {10.1016/j.cub.2025.07.069},
pmid = {40925330},
issn = {1879-0445},
mesh = {*Symbiosis/physiology ; *Root Nodules, Plant/microbiology/metabolism/physiology ; *Glycine max/microbiology/physiology/metabolism ; Nitrogen Fixation ; *Sucrose/metabolism ; Plant Root Nodulation ; Plant Proteins/metabolism/genetics ; Plant Roots/microbiology/metabolism ; },
abstract = {A new study shows that sucrose allocation within soybean roots by the sucrose transporter GmSWEET3c promotes rhizobial infection, nodulation, and symbiotic nitrogen fixation.},
}

*Symbiosis/physiology
*Root Nodules, Plant/microbiology/metabolism/physiology
*Glycine max/microbiology/physiology/metabolism
Nitrogen Fixation
*Sucrose/metabolism
Plant Root Nodulation
Plant Proteins/metabolism/genetics
Plant Roots/microbiology/metabolism

@article {pmid40925006,
year = {2025},
author = {Hu, Y and Moreau, CS},
title = {Nutritional Symbiosis Between Ants and Their Symbiotic Microbes.},
journal = {Annual review of entomology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-ento-121423-013513},
pmid = {40925006},
issn = {1545-4487},
abstract = {Nutritional symbioses with microorganisms have profoundly shaped the evolutionary success of ants, enabling them to overcome dietary limitations and thrive across diverse ecological niches and trophic levels. These interactions are particularly crucial for ants with specialized diets, where microbial symbionts compensate for dietary imbalances by contributing to nitrogen metabolism, vitamin supplementation, and the catabolism of plant fibers and proteins. This review synthesizes recent advances in our understanding of ant-microbe symbioses, focusing on diversity, functional roles in host nutrition, and mechanisms of transmission of symbiotic microorganisms. Despite progress, most research has concentrated on a few ant genera, and further exploration of microbial roles in different ant morphs and life stages and across various ant species is needed. Expanding research to include a broader array of ant lineages and integrating genomic data with additional experimental data will provide deeper insights into the metabolic strategies that facilitate ant success across diverse ecological habitats.},
}

@article {pmid40924927,
year = {2025},
author = {Colombo, M},
title = {Cognitive Symbionts. Expanding the Scope of Cognitive Science With Fungi.},
journal = {Topics in cognitive science},
volume = {},
number = {},
pages = {},
doi = {10.1111/tops.70024},
pmid = {40924927},
issn = {1756-8765},
abstract = {It has been argued that fungi have cognitive capacities, and even conscious experiences. While these arguments risk ushering in unproductive disputes about how words like "mind," "cognitive," "sentient," and "conscious" should be used, paying close attention to key properties of fungal life can also be uncontroversially productive for cognitive science. Attention to fungal life can, for example, inspire new, potentially fruitful directions of research in cognitive science. Here, I introduce a concept of cognitive symbiosis whose significance for cognitive science becomes salient when we consider the centrality of symbioses in the life of fungi. Like fungi, virtually all cognitive systems live in close association with other kinds of cognitive systems, and this living together can have substantive psychological consequences. Expanding the scope of cognitive science to study a wide variety of cognitive symbioses underwrites the importance of biology and evolution in understanding minds.},
}

@article {pmid40924749,
year = {2025},
author = {Amoros, J and Buysse, M and Floriano, AM and Moumen, B and Vavre, F and Bouchon, D and Duron, O},
title = {Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts.},
journal = {PLoS genetics},
volume = {21},
number = {9},
pages = {e1011856},
doi = {10.1371/journal.pgen.1011856},
pmid = {40924749},
issn = {1553-7404},
abstract = {Cytoplasmic Incompatibility (CI) causes embryonic lethality in arthropods, resulting in a significant reduction in reproductive success. In most cases, this reproductive failure is driven by Wolbachia endosymbionts through their cifA/cifB gene pair, whose products disrupts arthropod DNA replication during embryogenesis. While a cif pair has been considered a hallmark of Wolbachia, its presence and functional significance in other bacterial lineages remains poorly investigated. Here, we conducted a comprehensive survey of 762 genomes spanning non-Wolbachia endosymbionts and their close relatives, revealing that the cif pair is far more widespread than previously recognized. We identified cif loci in 8.4% of the surveyed genomes, with a striking incidence of 17.4% in facultative symbionts. Beyond Wolbachia, cif pair occurs across eight bacterial genera spanning α-Proteobacteria, γ-Proteobacteria, Mollicutes, and Bacteroidota. Notably, cif pair has been identified in several intracellular pathogens of mammals showing high rate of transovarial transmission in their arthropod hosts, suggesting a potential role of cif pair and CI in vector-borne disease dynamics. Structural analyses further reveal that the PD(D/E)-XK nucleases and AAA-ATPase-like motifs are consistently conserved across cif pairs in all bacterial taxa. Moreover, cif pairs are frequently integrated within diverse mobile genetic elements, from transposons to large intact WO prophages in Wolbachia and RAGEs in Rickettsiaceae. Phylogenetic analyses reveal recent and potentially ongoing horizontal transfers of cif pair between distantly related bacterial lineages, a process potentially facilitated by mobile genetic elements. Indeed, the PDDEXK2 transposase exhibits a phylogenetic pattern consistent with the co-transmission of cif genes, suggesting that it may facilitate horizontal transfers of cif across bacterial lineages. Furthermore, the detection of endosymbionts harboring cif pair in arthropod groups where Wolbachia is scarce, such as ticks, suggests that CI may be more widespread than previously known, with significant implications for arthropod symbiosis, reproductive manipulation, and future biocontrol strategies.},
}

@article {pmid40924454,
year = {2025},
author = {Finegan, C and Kates, HR and Guralnick, RP and Soltis, PS and Resende, MFR and Ané, JM and Kirst, M and Folk, RA and Soltis, DE},
title = {Convergent evolution of NFP-facilitated root nodule symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2424902122},
doi = {10.1073/pnas.2424902122},
pmid = {40924454},
issn = {1091-6490},
support = {DE-SC0018247//US Department of Energy/ ; },
mesh = {*Symbiosis/genetics/physiology ; Phylogeny ; *Root Nodules, Plant/microbiology/genetics ; *Medicago truncatula/genetics/microbiology ; *Evolution, Molecular ; *Plant Proteins/genetics/metabolism ; Nitrogen Fixation ; Lipopolysaccharides/metabolism ; Biological Evolution ; },
abstract = {The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception (NFP) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP, indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1, located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1, likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2-like group are not orthologous, indicating multiple independent gains of NFP-based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.},
}

*Symbiosis/genetics/physiology
Phylogeny
*Root Nodules, Plant/microbiology/genetics
*Medicago truncatula/genetics/microbiology
*Evolution, Molecular
*Plant Proteins/genetics/metabolism
Nitrogen Fixation
Lipopolysaccharides/metabolism
Biological Evolution

@article {pmid40922700,
year = {2025},
author = {Wang, S and Wang, X and Adeniji, OD and Batchelor, WD and Wang, Y and Blersch, D and Higgins, BT and Liles, MR and Luo, W and Chen, CY and Feng, Y and Wang, Y},
title = {Targeted Genome Editing of the ACC Deaminase Gene in Bradyrhizobium: Toward Enhanced Plant Growth and Stress Tolerance.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70064},
pmid = {40922700},
issn = {1097-0290},
support = {//This study was supported by the National Peanut Board award (APPA-RIA16-PID 488 BID 1664)./ ; },
abstract = {Ensuring sufficient crop yields in an era of rapid population growth and limited arable land requires innovative strategies to enhance plant resilience and sustain, or even improve, growth and productivity despite environmental stress. Besides symbiotic nitrogen fixation, rhizobia may play a central role in sustainable agriculture by alleviating the detrimental effects of ethylene-a key stress hormone in plants-especially under conditions like drought through the deamination of 1-aminocyclopropane-1-carboxylic acid (ACC). In this study, we focused on genetically engineering a new Bradyrhizobium sp. isolate (Strain 9) from peanut root nodules to enhance its ACC deaminase activity. First, we developed a sacB-based genome-engineering tool and used it to knock out the ACC deaminase gene (acdS), confirming that its disruption severely diminished the strain's capacity to degrade ACC. Subsequently, we constructed an acdS-overexpressing strain by integrating a strong promoter and an optimized ribosome binding site upstream of acdS, achieving a five-fold increase in ACC deaminase activity relative to the wild-type. Peanut inoculation experiments demonstrated that both the acdS knockout and overexpression mutants effectively nodulated roots without impairing plant growth and nitrogen fixation, indicating that these modifications did not compromise symbiosis. Overall, this study highlights the utility of sacB-mediated counter-selection for precise genome editing in Bradyrhizobium and underscores the potential of enhanced ACC deaminase activity to improve plant growth under stress conditions. These findings pave the way for developing next-generation bioinoculants with superior ethylene mitigation capabilities, contributing to more productive and sustainable crop systems.},
}

@article {pmid40920925,
year = {2025},
author = {Marks, JC and Zampini, MC and Fitzpatrick, R and Kariunga, SH and Sitati, A and Samo, TJ and Weber, PK and Thomas, S and Hungate, BA and Ramon, CE and Wulf, M and Leshyk, VO and Schwartz, E and Pett-Ridge, J and Power, ME},
title = {Ecosystem consequences of a nitrogen-fixing proto-organelle.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2503108122},
doi = {10.1073/pnas.2503108122},
pmid = {40920925},
issn = {1091-6490},
support = {2125088//NSF (NSF)/ ; DE-AC52-07NA27344//US Department of Energy/ ; },
mesh = {*Nitrogen Fixation/physiology ; *Ecosystem ; *Symbiosis/physiology ; Nitrogen/metabolism ; Animals ; Food Chain ; Rivers ; *Diatoms/metabolism/physiology ; Carbon/metabolism ; Seasons ; Cyanobacteria/metabolism/physiology ; Nitrogen Isotopes ; Carbon Isotopes ; },
abstract = {Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.},
}

*Nitrogen Fixation/physiology
*Ecosystem
*Symbiosis/physiology
Nitrogen/metabolism
Animals
Food Chain
Rivers
*Diatoms/metabolism/physiology
Carbon/metabolism
Seasons
Cyanobacteria/metabolism/physiology
Nitrogen Isotopes
Carbon Isotopes

@article {pmid40919919,
year = {2025},
author = {Luo, Y and Srinivas, A and Guidry, C and Bull, C and Haney, CH and Hamilton, C},
title = {GacA regulates symbiosis and mediates lifestyle transitions in Pseudomonas.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0027725},
doi = {10.1128/msphere.00277-25},
pmid = {40919919},
issn = {2379-5042},
abstract = {Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the brassicacearum/corrugata/mediterranea (BCM) subclade of Pseudomonas fluorescens, including Pseudomonas species N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. Pseudomonas sp. N2E2 is a plant commensal and contains genes encoding biosynthetic enzymes for the antifungal compound 2,4-diacetylphloroglucinol (DAPG). In contrast, Pseudomonas sp. N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)- and syringopeptin (SYP)-like toxins from the plant pathogen Pseudomonas syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant-pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle. Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.IMPORTANCEEmerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer (HGT) aids in the acquisition of novel genes that facilitate adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT. These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. This work provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.},
}

@article {pmid40919716,
year = {2025},
author = {Xie, T and Lv, J and Wang, L and Wu, H and Chen, Y and Chen, R and Pan, H},
title = {Uninfected cell-specific enzymes coordinate carbon supply and nitrogen assimilation in Medicago truncatula nodules.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70560},
pmid = {40919716},
issn = {1469-8137},
support = {2024JJ2014; 2025ZYJ003//Natural Science Foundation of Hunan Province/ ; 32441035//National Natural Science Foundation of China/ ; 32470255//National Natural Science Foundation of China/ ; },
abstract = {In legume root nodules, rhizobia invade host cells to form symbiosomes that drive atmospheric nitrogen fixation. Although the metabolic roles of infected cells (ICs) are well established, the contributions of adjacent uninfected cells (UCs) have remained largely unexplored. Here, through forward genetics methods, we identify DEBINO4, a phosphoenolpyruvate carboxylase (PEPC) uniquely expressed in UCs, as a pivotal regulator of carbon metabolism essential for sustaining symbiosome function and nitrogen assimilation. DEBINO4-deficient mutants display premature nodule senescence characterized by nonviable symbiosomes in the fixation zone and disrupted carbon and nitrogen metabolic profiles. The nodule-specific PEPC kinases (PPCKs), which are probably involved in DEBINO4 activation, are required to preserve symbiosome integrity, while Glutamine Synthetase 1a (GS1a), also restricted to UCs, is critical for ammonium assimilation and maintaining differentiated symbiosomes. Comprehensive analysis of metabolism-related genes further reveals that UCs execute specialized, stage-specific functions during nitrogen fixation. Collectively, our findings underscore the importance of cell-type-specific metabolic networks in orchestrating successful symbiosis and provide a framework for understanding how distinct nodule cell populations coordinate carbon and nitrogen metabolism to support efficient nitrogen fixation.},
}

@article {pmid40919702,
year = {2025},
author = {Zhang, L and Tian, Y and Li, L and Zhan, W and Sun, H and Ren, N and Tang, Z and Ngo, HH},
title = {Movement Mechanisms Harness Lévy Flight for Energy-Efficient Wastewater Treatment in Microalgae-Bacteria Systems.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04676},
doi = {10.1002/advs.202504676},
pmid = {40919702},
issn = {2198-3844},
support = {52341001//National Natural Science Foundation of China/ ; 2022M710953//Postdoctoral Research Foundation of China/ ; 2022ZX02C16//Heilongjiang Key R&D Programme/ ; ES202424//The Open Project of State Key Laboratory of Urban Water Resources and Environment/ ; },
abstract = {Microalgae-bacteria symbiosis system is significant for sustainable and low-carbon wastewater treatment, with self-aggregation being key to its stable operation and effective pollutant removal. Cellular motility is the main driving force behind self-aggregation, crucial for symbiosis stability, but the characteristics and patterns involved still remain largely unexplored. Here, cellular movement dynamics into the microalgae-activated sludge model (ASM3) is incorporated, enabling synchronized simulation of metabolic activities and movement behaviors through physical and biochemical interactions in bioreactor systems. These findings indicate that microalgae induce bacterial movement towards Lévy flights, thereby increasing the bacterial encounter rate by 12.20%, augmenting signaling molecule concentration and biomass by 20.0% and 27.3%, respectively, which in turn strengthens the bacteria self-aggregation effect. Through practical reactor operations with metagenomic analysis, the efficacy of this model in elucidating self-aggregation is further corroborated, improving system stability and pollutant removal efficiency. An optimized microalgae-bacteria system reduces energy costs associated with cellular aggregation processes, economizing on the cost of chemotaxis-related proteins. This study not only elucidate the unique role of Lévy flight in self-aggregation, enhancing the understanding of microalgae-bacteria symbiosis, but also establish response mechanisms between motility patterns and operation dynamics. This allows for targeted regulation across various biosystems, ensuring cost-effective wastewater treatment and proactive prediction.},
}

@article {pmid40917997,
year = {2025},
author = {Meng, G and Li, J and Cao, Y and Li, F and Liu, M and Li, R and Dong, C},
title = {Haplotype-resolved genomes of Phlebopus portentosus reveal nuclear differentiation, TE-mediated variation, and saprotrophic potential.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e161411},
pmid = {40917997},
issn = {2210-6340},
abstract = {Phlebopus portentosus is a widely consumed edible mushroom and the only Boletales species currently cultivated on an industrial scale. Despite its economic importance, its trophic strategy and genomic adaptations remain elusive. Here, we presented high-quality, chromosome-level genome assemblies for two sexually compatible monokaryons (PP78 and PP85) of P. portentosus. Comparative genomic analysis revealed a genome size difference of 1.17 Mb (30.87 vs. 32.04 Mb), primarily attributed to transposable element (TE) expansion in strain PP85. Genome structural variations were largely driven by TEs, particularly LTR retrotransposons. DNA transposons were also involved in structural rearrangement of secondary metabolite biosynthetic gene clusters, impacting their organization and transcriptional profiles. Functional annotation identified 187 PP78-specific and 236 PP85-specific genes, with the latter enriched in TE-related and putative virulence factors. P. portentosus displays genomic signatures of both ECM symbiosis (reduced lignocellulose-degrading enzymes) and saprotroph (expanded glycoside hydrolase 31 and sugar transporters), supporting a facultative ECM lifestyle. The expansion of non-ribosomal peptide synthetase and polyketide synthase pathways, alongside contraction of terpenoid clusters typical of ECM fungi, further indicated its adaptation to saprotroph. These findings highlight the role of TEs in driving genome plasticity, metabolic diversity, and nuclear divergence in P. portentosus, providing valuable genomic resources for this species.},
}

@article {pmid40917749,
year = {2025},
author = {Fu, L and Wang, M and Li, D and Ma, S and Zhang, F and Zheng, L},
title = {Microbial metabolites short chain fatty acids, tight junction, gap junction, and reproduction: a review.},
journal = {Frontiers in cell and developmental biology},
volume = {13},
number = {},
pages = {1624415},
pmid = {40917749},
issn = {2296-634X},
abstract = {The gut microbiota, comprising trillions of bacteria, fungi, and viruses, exists in symbiosis with the host. As the largest microbial ecosystem in the human body. The gut microbiota not only shapes the homeostasis of the intestinal microenvironment through gut-derived metabolites but also exerts regulatory effects on the functions of diverse tissues and organs throughout the body via the intricate "gut-distal organ axis" mechanism. Short chain fatty acids, such as acetic acid, propionic acid and butyric acid are high abundance intestinal metabolites, not only influence the intestinal barrier by regulating tight junction proteins, but also affect intestinal peristalsis by regulating gap junction proteins. These microbial metabolites may also play a important role in the formation and maintenance of the key barriers of the reproductive system, such as the ovarian blood follicle barrier, the testicular blood-testis barrier, and the endometrial epithelial barrier. In reproductive system, Gap junction-mediated intercellular communication, facilitated by connexins, proves essential in germ cell maturation, embryo implantation, and spermatogenesis. The dysregulation of these microbial metabolites leading to abnormal tight junction and gap junction protein functions provides novel perspectives for understanding the pathogenesis of reproductive disorders such as polycystic ovary syndrome and premature ovarian failure. This review systematically elucidates the molecular networks through which short-chain fatty acids regulate tight and gap junction proteins, highlighting their potential roles in reproductive physiology.},
}

@article {pmid40916562,
year = {2025},
author = {Sharoni, T and Jaimes-Becerra, A and Lewandowska, M and Aharoni, R and Voolstra, CR and Fine, M and Moran, Y},
title = {Heat Stress Drives Rapid Viral and Antiviral Innate Immunity Activation in Hexacorallia.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70098},
doi = {10.1111/mec.70098},
pmid = {40916562},
issn = {1365-294X},
support = {863809//H2020 European Research Council/ ; },
abstract = {The class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. Here the model sea anemone Nematostella vectensis is used to explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor genes involved in antiviral responses. Under heat stress, the reporter genes showed significant upregulation. Further, transcriptomes from N. vectensis, Exaiptasia diaphana and the stony coral Stylophora pistillata were analysed to reveal stress-induced activation of a set of bona fide immune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in both Nematostella and Stylophora, depending on geographic origin. In Exaiptasia, the presence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves contribute to this immune response under stress, we subjected N. vectensis to heat stress and measured the transcription dynamics of resident viruses as well as selected antiviral genes. While the antiviral genes responded within hours of heat stress, viral gene expression was already upregulated within 30 min, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the interplay between environmental stress, viruses, immune responses and symbiotic states in Hexacorallia.},
}

@article {pmid40915801,
year = {2025},
author = {Xue, H and Qiao, X and Du, L and Wang, L and Zhang, K and Li, D and Ji, J and Cui, J and Zhu, X and Luo, J and Gao, X},
title = {Host-microbe synergy in pesticide resilience: Rhodococcus-driven fitness compensation in chlorpyrifos-stressed Binodoxys communis.},
journal = {Pesticide biochemistry and physiology},
volume = {214},
number = {},
pages = {106609},
doi = {10.1016/j.pestbp.2025.106609},
pmid = {40915801},
issn = {1095-9939},
mesh = {*Chlorpyrifos/pharmacology/toxicity ; Animals ; *Rhodococcus/physiology/drug effects ; *Insecticides/pharmacology/toxicity ; *Aphids/drug effects ; *Host Microbial Interactions/drug effects ; Symbiosis ; },
abstract = {Chlorpyrifos (CPF), a widely used organophosphate insecticide in cotton cultivation for controlling Aphis gossypii, has Binodoxys communis as the primary parasitic natural enemy of A. gossypii. This study evaluated the impact of two sub-lethal CPF concentrations (LC10 and LC30) on key biological parameters across two generations, transcriptomic responses, and symbiotic bacterial communities in B. communis. CPF exposure significantly reduced F1 generation survival by 39.89 % (LC10) and F2 generation survival by 33.31 % (LC30). Emergence rates were markedly decreased in both F1 (33.43 %) and F2 (19.86 %) generations under LC10 exposure. Furthermore, LC10 treatment significantly prolonged the F1 pre-pupal stage by 31.58 %. Short-term (1 h) CPF exposure markedly suppressed the expression of genes involved in energy metabolism, lipid metabolism, and PPAR signaling pathways. Notably, CPF exposure (both 1 h and 3 days) resulted in a significant increase in the relative abundance of Rhodococcus, suggesting a potential role of this bacterium in enhancing B. communis fitness under insecticide stress. Our findings not only inform the judicious application of CPF, but also identify molecular targets associated with energy and nutrient metabolism, while laying the groundwork for harnessing bacteria to enhance pesticide resistance in parasitoid wasps.},
}

*Chlorpyrifos/pharmacology/toxicity
Animals
*Rhodococcus/physiology/drug effects
*Insecticides/pharmacology/toxicity
*Aphids/drug effects
*Host Microbial Interactions/drug effects
Symbiosis

@article {pmid40894694,
year = {2025},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40894694},
issn = {2692-8205},
support = {P41 GM103399/GM/NIGMS NIH HHS/United States ; P41 GM136463/GM/NIGMS NIH HHS/United States ; P41 RR002301/RR/NCRR NIH HHS/United States ; T32 GM008349/GM/NIGMS NIH HHS/United States ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season.},
}

@article {pmid40919466,
year = {2025},
author = {Lian, J and Zou, D and Trebuch, LM and Duan, C and Li, M},
title = {Exploring the interactions between algae and archaea.},
journal = {Marine life science & technology},
volume = {7},
number = {3},
pages = {450-465},
pmid = {40919466},
issn = {2662-1746},
abstract = {Algae and archaea co-exist in diverse aquatic ecosystems and play a significant role in ecological functions and biogeochemical cycles. Compared to well-studied algal-bacterial interactions, there is a lack of information on algal-archaeal interactions and how their interactions affect their physiological fitness and nutrient cycles in either artificial cultivation systems or natural environments. The vast archaeal biodiversity, as indicated by genomic sequencing and computational approaches, has stimulated great interest in exploring uncultivated archaea to expand our knowledge of algae-archaea symbiosis. In this review, we summarize the latest studies on the diversity of algae-associated archaea and their (putative) symbiotic interactions, highlight the effects of algal-archaeal interactions on biogeochemical cycles and extend such knowledge to facilitate novel archaeal isolation and a broad range of algae-based biotechnological applications.},
}

@article {pmid40915677,
year = {2025},
author = {Costa, FF and Lustosa, BPR and Perico, CP and Belmonte-Lopes, R and Carvalho, JLVR and Razzolini, EL and Santos, GDD and Lima, BJFS and Souza-Motta, CM and Raittz, RT and Song, Y and Selbmann, L and de Hoog, GS and Meis, J and Vicente, VA},
title = {In silico search reveals the association of lichens with black yeast-like fungi in the order Chaetothyriales.},
journal = {Fungal biology},
volume = {129},
number = {6},
pages = {101618},
doi = {10.1016/j.funbio.2025.101618},
pmid = {40915677},
issn = {1878-6146},
mesh = {*Lichens/microbiology/classification ; *Ascomycota/genetics/classification/isolation & purification/physiology ; Metagenomics ; Symbiosis ; Phylogeny ; Computer Simulation ; Metagenome ; },
abstract = {Lichens exemplify a unique symbiotic relationship between fungi and algae or cyanobacteria, where fungi (mycobionts) provide structural support, while algae or cyanobacteria (photobionts) provide nutrients. Recent discoveries in the order Chaetothyriales have led to the description of several lichenicolous species, underscoring an intricate relationship of some black yeast-like fungi with lichens. The present study aims to investigate public metagenomic data of lichens available in the SRA database, covering a total of 2888 samples. The analysis incorporated 122 molecular marker sequences (barcodes and padlock probes) previously documented in the literature for species classified within Chaetothyriales. Additionally, 11 novel barcodes for species recently identified in lichens of the genera Cladophialophora and Paracladophialophora are described. The selected metagenomes were then compared with molecular marker sequences using local BLASTn (v2.6.0+), considering only alignments with a coverage cut-off and 100 % identity (perfect match). Reads from each sample were retrieved from the SRA as a multifasta file and analyzed with the SWeeP method for vector-based, alignment-free sequence analysis. The analysis identified fungi that are known as environmental inhabitants and, occasionally, opportunistic pathogens of vertebrates, including species in the genera Cladophialophora, Cyphellophora, and Exophiala. These species were distributed across 11 BioProjects from various locations around the world. The findings of this study corroborate extant knowledge concerning fungal colonization in diverse extremophilic environments, including deserts, tundra, and rocky surfaces.},
}

*Lichens/microbiology/classification
*Ascomycota/genetics/classification/isolation & purification/physiology
Metagenomics
Symbiosis
Phylogeny
Computer Simulation
Metagenome

@article {pmid40915132,
year = {2025},
author = {Shu, P and Zhao, L and Wen, X and Wei, Z and Yuan, C and Liu, H and Zhang, X and Long, X and He, Q and Li, W},
title = {Iron oxide-mediated enhancement of extracellular electron transfer and symbiosis in consortium of electroactive bacteria and microalgae for wastewater treatment.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124516},
doi = {10.1016/j.watres.2025.124516},
pmid = {40915132},
issn = {1879-2448},
abstract = {This study explores the role of α-Fe2O3 in improving extracellular electron transfer (EET) and symbiotic interactions between electroactive Shewanella oneidensis MR-1, its gene-deficient mutants (ΔmtrC, ΔomcA, and ΔcymA), and microalgae (Chlorella vulgaris). The iron oxide facilitates the efficient transfer of electrons generated by MR-1 to microalgal photosystem via the pathway of CymA-MtrC-OmcA to α-Fe2O3. This process enhances the removals of TOC, TN, and NH4[+]-N in the MR-1 bacterial-algal consortium by 9.99%, 12.32%, and 52.25% respectively via OmcA regulation while boosting phosphorus removal by 16.27% through CymA regulation. The consortium exhibits 26.76% lower CO2 emission and 62.93% higher biomass productivity. When integrated into microbial fuel cells with ΔcymA mutants, α-Fe2O3 elevates open-circuit voltage by 283.33%, confirming its ability to compensate for electron deficiencies caused by CymA defects. α-Fe2O3 enhances energy metabolisms (TCA cycle, quinone pool, and photosynthesis) to modulate the key metabolites including starch/sucrose, glycolysis, amino acids, lipids, and quorum sensing. These adaptations strengthen the symbiotic interactions and utilization of MR-1 bacterial-algal consortium for carbon and nutrients. Reactor experiments validate that α-Fe2O3 integration with the consortium achieves 93.43% COD removal and 55.99% NH4[+]-N removal, while reducing N2O emissions by 61.37%. The results reveal the interplay between OmcA, CymA, and iron oxides in optimizing bacterial-algal consortia and underscore the molecular mechanisms underlying iron oxide-enhanced EET for developing low-carbon, resource-efficient wastewater treatment.},
}

@article {pmid40915025,
year = {2025},
author = {Ortiz, J and Sanhueza, C and Romero-Munar, A and Sierra, S and Palma, F and Aroca, R and de la Peña, TC and López-Gómez, M and Bascuñán-Godoy, L and Del-Saz, NF},
title = {Nitrogen source and availability associate to mitochondrial respiratory pathways and symbiotic function in Lotus japonicus.},
journal = {Journal of plant physiology},
volume = {314},
number = {},
pages = {154606},
doi = {10.1016/j.jplph.2025.154606},
pmid = {40915025},
issn = {1618-1328},
abstract = {Legumes form symbioses with nitrogen-fixing bacteria, well studied metabolically but less so in terms of respiration. Symbiotic nitrogen fixation demands high respiratory ATP and carbon skeletons, linking nitrogen assimilation and both NADH- and ATP-dependent process to mitochondrial respiration. The plant mitochondrial electron transport chain contains two terminal oxidases that differentially fractionate against [18]O, providing estimations in vivo of the energy efficiency of respiration. The regulation of N2 fixation by plant respiratory parameters remains unknown. To investigate the regulatory interactions of these two metabolic processes, we tested the effect of different plant N status and sources on respiratory parameters and nutrition in Lotus japonicus. Plants were grown with two levels of KNO3 fertilization (5 mM and 25 mM) and with the N2 fixing symbiotic bacteria Mesorhizobium loti, which induced the formation of root nodules (NP). Additionally, we characterized roots containing non-fixing nodules by growing plants that display spontaneous nodule formation (snf) (SNF). We evaluated the natural abundances of [13]C and [15]N, and [18]O discrimination during respiration in leaves and roots using isotope-ratio mass spectrometry. NADH and nutrient content were measured using ultra-performance liquid chromatography and inductively coupled plasma spectrometry. We observed that cytochrome c oxidase activity was higher in nodulated roots capable of nitrogen fixation than in plants fertilized with high availability of nitrate, and that nitrogen status strongly associates to respiratory parameters. These findings highlight the role of cytochrome c oxidase in meeting the carbon and energy demands of symbiotic nitrogen fixation.},
}

@article {pmid40914954,
year = {2025},
author = {Gao, Y and Wu, Y and Chang, P and Li, P and Hu, S and Liu, L},
title = {Mycorrhizal Network and Symbiotic N-Fixer Jointly Enhance the Interplant Nitrogen Sharing.},
journal = {Ecology letters},
volume = {28},
number = {9},
pages = {e70204},
doi = {10.1111/ele.70204},
pmid = {40914954},
issn = {1461-0248},
support = {2022YFF1301701//National Key Research and Development Program of China/ ; 32125025//National Natural Science Foundation of China/ ; 32330066//National Natural Science Foundation of China/ ; },
mesh = {*Symbiosis ; *Mycorrhizae/physiology ; *Nitrogen/metabolism ; *Nitrogen Fixation ; *Nitrogen-Fixing Bacteria/physiology/metabolism ; },
abstract = {Symbioses with mycorrhizal fungi and nitrogen-fixing bacteria (NFB) enhance nitrogen (N) acquisition in host plants and may promote N transfer to neighbouring plants through mycorrhizal networks (MN). Nevertheless, the extent and mechanisms of this transfer remain unclear. On the basis of a synthesis of [15]N labeling studies, we show that MN and NFB synergistically enhanced interplant N sharing. In the presence of MN, N transfer from N-fixing donors to non-N-fixing receivers increased by an average of 9.7-fold, accounting for 5.61% of the total N in receiver plants. Moreover, greater amounts of N were transferred from N-fixing plants towards their phylogenetically distant plants. Source-sink gradients driven by differences in N content between neighbouring plants further promoted N transfer. Together, our findings highlight the ecological significance of an expanded MN framework in explaining interplant N sharing and provide new insights into how symbiotic guild interactions promote species coexistence and biodiversity maintenance.},
}

*Symbiosis
*Mycorrhizae/physiology
*Nitrogen/metabolism
*Nitrogen Fixation
*Nitrogen-Fixing Bacteria/physiology/metabolism

@article {pmid40914099,
year = {2025},
author = {Havlik, MN and Geraldi, NR and Hopkins, LW and Hubert, J and Chapuis, L and Gaffney, LP and Wilson, RP and Simpson, SD and Juanes, FJ and Duarte, CM},
title = {Boat noise alters behaviour of two coral reef macroinvertebrates, Lambis lambis and Tridacna maxima.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 1},
pages = {118650},
doi = {10.1016/j.marpolbul.2025.118650},
pmid = {40914099},
issn = {1879-3363},
abstract = {Boat noise has been shown to distract and cause harm to many marine organisms. Most of the study effort has focused on fish & marine mammals, even though invertebrates represent over 92 % of all marine life. The few studies conducted on invertebrates have demonstrated clear negative effects of anthropogenic noise pollution. The small giant clam Tridacna maxima and the spider conch Lambis lambis are two invertebrate species which play key roles in coral reef ecosystems, and are little studied for the effects of noise disturbance. T. maxima functions as prey for many fish species, contributes up to 9 % of the reef's calcium carbonate budget, and plays a role in nutrient cycling. The herbivorous strombid L. lambis can occur in large numbers on reef flats and is prey for other snails and several elasmobranchs. Using two case study reefs, we show that both boat noise and biotic sounds are prominent sound sources in Red Sea reef habitats. In-situ controlled exposure experiments were conducted on two shallow central Red Sea reefs, where Daily Diary smart tags were used to measure the reactions of T. maxima and L. lambis during underwater playback of boat noise and ambient reef sound. Both macroinvertebrates exhibited behavioral changes during the boat noise treatment. Our results suggest that L. lambis and T. maxima individuals may spend energy averting the invisible "threat" of boat noise, rather than feeding or staying open for symbiotic algae to perform photosynthesis, in the case of T. maxima. As boat noise is prevalent on Red Sea reefs, invertebrates may be affected on a large scale in the Red Sea.},
}

@article {pmid40913714,
year = {2025},
author = {Lopes, MR and Direito, R and Guiguer, EL and Catharin, VCS and Zutin, TLM and Rubira, CJ and Catharin, VMCS and Sloan, KP and Sloan, LA and Junior, JLY and Laurindo, LF and Barbalho, SM and de Alvares Goulart, R},
title = {Bridging the Gut Microbiota and the Brain, Kidney, and Cardiovascular Health: The Role of Probiotics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40913714},
issn = {1867-1314},
abstract = {The symbiosis between intestinal bacteria and the human body's physiological processes can modulate health. The intestinal microbiota is linked to the development of neurotrophic factors; therefore, it is increasingly related to the modulation of nervous system pathologies. Moreover, microbiota can interfere with inflammation and oxidative stress, which are closely linked to cardiovascular risk factors and several other inflammatory conditions, such as kidney and neurodegenerative diseases. Probiotics are live microorganisms that help regulate and maintain healthy microbiota; thus, they can help prevent these diseases. Due to these reasons, this review aimed to evaluate the effects of probiotics on the gut, kidneys, brain, and heart homeostasis. Clinical trials showed several positive results with the treatment. In the brain, probiotics reduce depressive symptoms (decreases in HAMA, GAD-7, and BDI-II scales), improving patients' sleep quality and fatigue, enhancing cognitive subscales while slowing brain atrophy, and reducing IL-6 levels in the central areas, also modulating REM delta power to reduce high-frequency brain waves. Probiotics can also reduce cardiovascular risk factors, such as inflammation. Probiotics can also benefit the heart by decreasing TMAO, LDL-c, TG, CRP, MDA, TNF-α, IL-6, and urea levels, improving dyslipidemia and toxin profiles. Probiotics also increase HDL-c, ApoE, and insulin sensitivity, decreasing BMI, body fat, and the risk of developing chronic hyperglycemia while increasing lean mass. Besides, probiotic supplementation helped reduce toxic uremic toxins (serum urea) and sodium levels, bringing benefits to the kidneys, and improve energy/amino acid metabolism. Probiotics can also modulate and enhance kidney function due to decreased pro-inflammatory TGFβ-1 and TNF-α levels and RUNX2. Furthermore, enhanced gastrointestinal motility and diversity have been reported using specific bacteria. Although probiotics can bring several health benefits, there are still challenges regarding these supplements, such as dose, frequency, and pharmaceutical formula. Therefore, new studies are welcome to deepen the understanding of these microorganisms.},
}

@article {pmid40913463,
year = {2025},
author = {Mostafa, KM and Cheng, YH and Chu, LW and Nguyen, PT and Liu, CJ and Liao, CW and Posch, T and Leu, JY},
title = {Environment-dependent mutualism-parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf203},
pmid = {40913463},
issn = {1751-7370},
abstract = {Mutualistic endosymbiosis is a cornerstone of evolutionary innovation, enabling organisms to exploit diverse niches unavailable to individual species. However, our knowledge about the early evolutionary stage of this relationship remains limited. The association between the ciliate Tetrahymena utriculariae and its algal endosymbiont Micractinium tetrahymenae indicates an incipient stage of photoendosymbiosis. Although T. utriculariae cells rely on endosymbiotic algae to grow in low-oxygen conditions, they gradually lose the endosymbionts in oxic conditions. In this study, comparative phylogenomics revealed accelerated evolution in mitochondrial DNA and nucleus-encoded mitochondrial genes in T. utriculariae. Symbiotic cells displayed elongated mitochondria that interacted intimately with endosymbionts. Inhibition of mitochondrial fatty acid oxidation reduced host fitness but increased the endosymbiont population. Time-series transcriptomics revealed physiological fine-tuning of the host across day-night cycles, highlighting symbiosis-associated regulatory adjustments. Endosymbiotic algae downregulated photosynthesis-related genes compared with free-living cells, which correlated with reduced chlorophyll content, suggesting a shift toward host resource exploitation to compensate for diminished photosynthetic capacity. Under oxic conditions, symbiotic T. utriculariae cells exhibited lower fitness than aposymbiotic cells. Our results demonstrate that incipient endosymbioses employ mitochondrial remodeling and endosymbiont metabolic reprogramming to actively regulate transitions between mutualistic and parasitic states, revealing how symbiotic partnerships navigate environmental pressures during their incipient stage of evolutionary establishment.},
}

@article {pmid40913088,
year = {2025},
author = {Chandola, U and Manirakiza, E and Maillard, M and Lavier Aydat, LJ and Camuel, A and Trottier, C and Tanaka, A and Chaumier, T and Giraud, E and Tirichine, L},
title = {A Bradyrhizobium isolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40913088},
issn = {2058-5276},
abstract = {Biological nitrogen fixation converts atmospheric nitrogen into ammonia, essential to the global nitrogen cycle. While cyanobacterial diazotrophs are well characterized, recent studies have revealed a broad distribution of non-cyanobacterial diazotrophs (NCDs) in marine environments, although their study is limited by poor cultivability. Here we report a previously uncharacterized Bradyrhizobium isolated from the marine diatom Phaeodactylum tricornutum. Phylogenomic analysis places the strain within photosynthetic Bradyrhizobium, suggesting evolutionary adaptations to marine and terrestrial niches. Average nucleotide identity supports its classification as a previously undescribed species. Remarkably, inoculation experiments showed that the isolate induced nitrogen-fixing nodules in the Aeschynomene indica legume, pointing to symbiotic capabilities across ecological boundaries. Pangenome analysis and metabolic predictions indicate that this isolate shares more features with terrestrial photosynthetic Bradyrhizobium than with marine NCDs. Overall, these findings suggest that symbiotic interactions could evolve across different ecological niches, and raise questions about the evolution of nitrogen fixation and microbe-host interactions.},
}

@article {pmid40911574,
year = {2025},
author = {Chang, ACG and Amaral, MWW and Greenwood, M and Ikudaisi, C and Li, J and Hamsher, SE and Miller, S and Kociolek, P},
title = {Evolutionary dynamics in plastomes and mitogenomes of diatoms.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331749},
doi = {10.1371/journal.pone.0331749},
pmid = {40911574},
issn = {1932-6203},
mesh = {*Diatoms/genetics/classification ; *Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; Pseudogenes ; },
abstract = {Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling, contributing significantly to photosynthesis and serving as fundamental components in aquatic ecosystems. Recent advancements in genomic sequencing have shed light on their evolutionary dynamics, revealing evolutionary complex genomes influenced by symbiotic relationships and horizontal gene transfer events. By analyzing publicly available sequences for 120 plastomes and 70 mitogenomes, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. Gene losses and pseudogenes were more frequently observed in plastomes compared with mitogenomes. Overall, gene losses were particularly abundant in the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp. Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC, ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost repeatedly across several diatom taxa. Analysis of nucleotide substitution rates indicated that, in general, mitogenomes were evolving at a more rapid rate compared to plastomes. This is contrary to what was observed in synteny analyses, where plastomes exhibited more structural rearrangements than mitogenomes, with the exception of the genus Coscinodiscus and one group of species within Thalassiosira.},
}

*Diatoms/genetics/classification
*Genome, Mitochondrial/genetics
*Evolution, Molecular
Phylogeny
Pseudogenes

@article {pmid40911442,
year = {2025},
author = {Tang, J and Yang, S and Li, S and Yue, X and Jin, T and Yang, X and Zhang, K and Yang, Q and Liu, T and Zhao, S and Gai, J and Li, Y},
title = {Editing a gibberellin receptor gene improves yield and nitrogen fixation in soybean.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70026},
pmid = {40911442},
issn = {1744-7909},
support = {32372192//National Natural Science Foundation of China/ ; JBGS-2021-014//Core Technology Development for Breeding Program of Jiangsu Province/ ; BM2024005//Jiangsu Key Laboratory of Soybean Biotechnology and Intelligent Breeding/ ; },
abstract = {Soybean is an important source of oil, protein, and feed. However, its yield is far below that of major cereal crops. The green revolution increased the yield of cereal crops partially through high-density planting of lodging-resistant semi-dwarf varieties, but required more nitrogen fertilizers, posing an environmental threat. Genes that can improve nitrogen use efficiency need to be integrated into semi-dwarf varieties to avoid the overuse of fertilizers without the loss of dwarfism. Unlike cereal crops, soybean can assimilate atmospheric nitrogen through symbiotic bacteria. Here, we created new alleles of GmGID1-2 (Glycine max GIBBERELLIN INSENSITIVE DWARF 1-2) using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) editing, which improved soybean architecture, yield, seed oil content, and nitrogen fixation, by regulation of important pathways and known genes related to branching, lipid metabolism, and nodule symbiosis. GmGID1-2 knockout reduced plant height, and increased stem diameter and strength, number of branches, nodes on the primary stem, pods, and seeds per plant, leading to an increase in seed weight per plant and yield in soybean. The nodule number, nodule weight, nitrogenase activity, and nitrogen content were also improved in GmGID1-2 knockout soybean lines, which is novel compared with the semi-dwarf genes in cereal crops. No loss-of-function allele for GmGID1-2 was identified in soybean germplasm and the edited GmGID1-2s are superior to the natural alleles, suggesting the GmGID1-2 knockout mutants generated in this study are valuable genetic resources to further improve soybean yield and seed oil content in future breeding programs. This study illustrates the pleiotropic functions of the GID1 knockout alleles with positive effects on plant architecture, yield, and nitrogen fixation in soybean, which provides a promising strategy toward sustainable agriculture.},
}

@article {pmid40911291,
year = {2025},
author = {Zhang, G and Yue, Y and Tu, L and Liu, Q and Zhang, Q and Shang, K},
title = {Responses of microbial communities during oilseed plant-based phytoremediation of heavy metal contaminated soils.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf226},
pmid = {40911291},
issn = {1365-2672},
abstract = {AIMS: Phytoremediation is an effective method of remediating soils contaminated with heavy metals. However, it has some limitations in practical applications with regard to rare plant species, poor environmental adaptability, and long growth cycles. The dynamic response mechanisms of soil microbial communities during phytoremediation are still unclear, which restricts the optimization and promotion of this approach.

METHODS AND RESULTS: No ethical approval was required for this study. In this study, soil bacterial, fungal, and archaeal communities during the remediation of Cu-, Pb-, and Zn-contaminated soils with five industrial oilseed plants (Xanthium strumarium (XS), Bidens pilosa (BP), Kosteletzkya virginica (KV), Sesbania cannabina (SC), and Commelina communis (CC)) were analyzed using metagenome sequencing. Compared with soil contaminated with heavy metals, remediation through five industrial oilseed plants significantly reduced the content of heavy metals in the soil, with soil Cu, Pb, and Zn decreasing by 44.01%, 46.32%, and 27.62%, respectively, and WSCu, WSPb, and WSZn content decreasing by 28.23%, 50.68%, and 75.26%, respectively. Microbial diversity analysis showed that phytoremediation significantly affected the soil microbial communities, with a significant decrease in archaeal diversity. Variation partitioning analysis and Mantel tests revealed that heavy metals and soil physicochemical properties significantly affected microbial communities, and heavy metals exerted stronger effects on archaeal communities. Meanwhile, soil contaminated with heavy metals was mainly dominated by fungal-fungal interactions, whereas phytoremediation increased the complexity of microbial symbiotic networks.

CONCLUSION: Collectively, these results provide fundamental insights into the microbial community structure during phytoremediation of heavy metal contaminated soil, which may aid in the bioregulation of phytoremediation.},
}

@article {pmid40911260,
year = {2025},
author = {Irum, S and Cilkiz, M and Al-Kubaisi, N and Elshikh, MS and Iqbal, R},
title = {Genome-wide characterization and expression analysis of the chitinase gene family in chickpea (Cicer arietinum L.) for fungal stress resistance.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {871},
pmid = {40911260},
issn = {1573-4978},
mesh = {*Cicer/genetics/microbiology/enzymology ; *Chitinases/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant/genetics ; *Disease Resistance/genetics ; Stress, Physiological/genetics ; Fusarium/pathogenicity ; Plant Diseases/microbiology/genetics ; Multigene Family ; Plant Proteins/genetics/metabolism ; Gene Expression Profiling/methods ; Genome, Plant ; },
abstract = {Chitinases, enzymes responsible for hydrolyzing chitin, a significant component of fungal cell walls, play a crucial role in plant defense mechanisms, growth, symbiotic relationships, and stress resistance. In this study, we identified 27 chitinase genes in chickpeas (CaChi) and classified them into five classes based on phylogenetic analysis. Overall, chitinase genes are clustered on eight chromosomes. Among these chromosomes (Chr), Chr-2 displayed the maximum number of genes. Meanwhile, promoter analysis revealed that cis-elements are involved in responses to phytohormones, biotic stress, plant growth, and development. Tissue-based expression analysis indicated that CaChi genes are predominantly expressed in the seedling and floral parts. Furthermore, qRT-PCR analysis revealed that CaChi genes play diverse roles in plant-environment interactions. Notably, several CaChi members were strongly induced by Fusarium oxysporum f. sp. and fourteen genes (CaChi20, CaChi25, CaChi11, CaChi3, CaChi16, CaChi14, CaChi1, CaChi4, CaChi5, CaChi8, CaChi9, CaChi21, CaChi18, CaChi13) exhibited elevated expression levels after post-inoculation, depicting a significant function of Chi genes in chickpea resistance to Fusarium wilt. These findings enhance understanding of the chitinase family in chickpea crops and clarify the functions of chickpea chitinase in response to fungal stress.},
}

*Cicer/genetics/microbiology/enzymology
*Chitinases/genetics/metabolism
Phylogeny
Gene Expression Regulation, Plant/genetics
*Disease Resistance/genetics
Stress, Physiological/genetics
Fusarium/pathogenicity
Plant Diseases/microbiology/genetics
Multigene Family
Plant Proteins/genetics/metabolism
Gene Expression Profiling/methods
Genome, Plant

@article {pmid40910153,
year = {2025},
author = {Chen, M and Raisin, A and Judkins, N and Allard, PM and Défossez, E and Stumpe, M and Yruela, I and Becana, M and Reinhardt, D},
title = {Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70494},
pmid = {40910153},
issn = {1469-8137},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia, Tecnología e Innovación/ ; 310030_200367//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; E35_23R//Gobierno de Aragón/ ; },
abstract = {In symbiotic plant-microbe interactions, the host invests considerable amounts of resources in the microbial partner. If the microbe does not reciprocate with a comparable symbiotic benefit, it is regarded as a cheater. The host responds to cheaters with negative feedback mechanisms (sanctions) to prevent fitness deficits resulting from being exploited. We study sanctioning in the symbiosis between Medicago truncatula and the nitrogen-fixing rhizobium Sinorhizobium meliloti. We manipulated the exchange of resources between the partners in three ways: by using mutant rhizobia defective in nitrogenase; replacing nitrogen in the atmosphere with argon gas; and supplying rich nitrogen fertilizer to the host. We follow the consequences of simulated cheating by examining the metabolome and proteome of both partners. We find that sanctioning occurs at multiple levels. In particular, we observe repression of essential symbiotic functions and changes in central metabolism that are likely to be relevant for microbial fitness and that could therefore contribute to sanctioning. In addition, sanctioning triggers a broad panel of defense markers. A thorough understanding of the multilevel phenomenon of sanctioning will be essential for its genetic dissection and for the breeding of elite legume crops with efficient symbiosis.},
}

@article {pmid40909766,
year = {2025},
author = {Bruzzese, DJ and Gstöttenmayer, F and Weiss, BL and Khalil, H and Mach, R and Abd-Alla, AMM and Aksoy, S},
title = {Comparative genomics and transcriptomics of the Spiroplasma glossinidia strain sGff reveal insights into host interaction and trypanosome resistance in Glossina fuscipes fuscipes.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7295611/v1},
pmid = {40909766},
issn = {2693-5015},
abstract = {Tsetse (Glossina spp.) are vectors of African trypanosomes, the causative agents of Human and African Animal trypanosomiases, diseases that remain significant medical and socioeconomic challenges in sub-Saharan Africa. In addition to trypanosomes, tsetse harbor both obligate and facultative symbiotic bacteria that can influence vector competence and reproductive biology. One such facultative symbiont, Spiroplasma glossinidia , infects several tsetse species within the Palpalis subgroup. In Glossina fuscipes fuscipes (Gff), the Spiroplasma glossinidia strain s Gff induces a trypanosome-refractory phenotype and negatively impacts reproductive fitness by reducing female fecundity. However, the mechanisms behind these Spiroplasma -derived phenotypes remain poorly understood. Here, we report successful in vitro cultivation of s Gff and present complete genomes from three sources: in vitro cultured s Gff and s Gff isolated from both laboratory-maintained and wild-caught (Uganda) Gff flies. Comparative genomic analyses revealed a high degree of similarity in gene content and synteny among these s Gff samples, confirming that they represent isolates of the same strain. Phylogenomic analyses placed s Gff within the Spiroplasma poulsonii clade. The s Gff genome is highly dynamic, containing numerous mobile genetic elements. Additionally, in silico annotations indicate that s Gff relies on its host for both lipids and carbohydrates and produces several toxins, all of which could be implicated in the observed trypanosome refractory phenotype. Finally, comparative transcriptomic analysis of s Gff from host hemolymph versus in vitro culture provided insights into potential factors relevant to host-symbiont interactions. Our findings provide a foundation for understanding the nutritional dialogue between s Gff and its host and identify symbiotic products that may contribute to trypanosome resistance. Furthermore, the establishment of an in vitro culture system for s Gff represents a significant resource for future functional studies with potential implications for vector control.},
}

@article {pmid40908936,
year = {2025},
author = {Oguchi, K and Munakata, M and Hiruta, C and Kakui, K},
title = {Intracellular Localization of the Bacterial Endosymbiont Cardinium in the Ostracod Heterocypris spadix.},
journal = {Zoological science},
volume = {42},
number = {4},
pages = {},
doi = {10.2108/zs250018},
pmid = {40908936},
issn = {0289-0003},
mesh = {Animals ; *Symbiosis ; *Crustacea/microbiology ; Female ; *Bacteroidetes/physiology ; },
abstract = {Symbiosis is a key driver of evolution in life-history traits and reproductive strategies. Some symbiotic microorganisms manipulate host reproduction to enhance their own transmission, a phenomenon well studied in insects but less understood in crustaceans. Among these microorganisms, Cardinium manipulates host reproductive systems, such as parthenogenesis, cytoplasmic incompatibility, and male killing in arthropods. However, its role in ostracods, small bivalve-shelled crustaceans, remains unclear. Some ostracod species reproduce via parthenogenesis, and high Cardinium infection rates in these lineages suggest a potential link between the symbiont and asexual reproduction. To investigate this relationship, we examined Cardinium localization in the parthenogenetic ostracod Heterocypris spadix from Japan. Using tissue clearing and fluorescence in situ hybridization (FISH), we visualized Cardinium within the ovaries. FISH observations revealed a widespread infection across the germarium, nurse cells, and oocytes. In early-stage oocytes, bacteria were evenly dispersed throughout the cytoplasm, whereas in more-developed oocytes, they clustered around the nucleus. Additionally, Cardinium was also detected in the hepatopancreas, indicating infection of both the reproductive and digestive systems. The presence of Cardinium in host reproductive structures, particularly the germarium, nurse cells, and developing oocytes, suggests its role in reproductive manipulation. To our knowledge, this study provides the first detailed localization of Cardinium in ostracods, reinforcing its potential influence on reproduction. Future research using antibiotics and genomic analysis will be crucial to confirm Cardinium's role in parthenogenesis induction.},
}

Animals
*Symbiosis
*Crustacea/microbiology
Female
*Bacteroidetes/physiology

@article {pmid40908830,
year = {2025},
author = {Yamlahi, YE and Remmal, I and Maurady, A and Britel, MR and Bakali, AH and Mokhtar, NB and Galiatsatos, I and Stathopoulou, P and Tsiamis, G},
title = {Characterization of the olive fly (Bactrocera oleae) microbiome across diverse geographic regions of Morocco.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70126},
pmid = {40908830},
issn = {1744-7917},
support = {22662//International Atomic Energy Agency/ ; },
abstract = {The olive fruit fly (Bactrocera oleae) is a significant pest threatening olive production worldwide. Bactrocera oleae relies on symbiotic bacteria for nutrition, development, and adaptation to its environment. Among these, Candidatus Erwinia dacicola is the most dominant symbiont and plays a key role in the fly's physiology and ecological adaptation. Understanding the dynamics between B. oleae, Ca. E. dacicola, and other components of the B. oleae microbiome is essential for developing effective targeted area-wide pest management strategies. This study aims to leverage full 16S rRNA gene sequencing to enhance the characterization of microbiome diversity in wild B. oleae populations from different regions in Morocco: Ouezzane, Rabat, Tanger, Errachidia, and Beni-Mellal. The results revealed distinct microbiome compositions influenced by geographic locations, with Candidatus Erwinia dacicola as the dominant symbiont, followed by Erwinia persicina as a secondary contributor. Other bacterial taxa, including Asaia bogorensis, were also identified, highlighting the functional diversity within the olive fly microbiome. These findings provide insights into the microbial ecology of B. oleae, contributing to the development and enhancement of sustainable pest control strategies.},
}

@article {pmid40908814,
year = {2025},
author = {Afonso, GVF and Johnson, GD and Collins, R and Pastana, MNL},
title = {Associations between fishes (Actinopterygii: Teleostei) and anthozoans (Anthozoa: Hexacorallia) in epipelagic waters based on in situ records.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70214},
pmid = {40908814},
issn = {1095-8649},
abstract = {We formally describe the association of fishes and anthozoans in epipelagic waters, extending this relationship to beyond the benthos. In situ observations and photographs of Aluterus schoepfii, Ariomma regulus, Caranx cf. latus and Brama spp. swimming alongside or holding larval tube anemones (Cerianthidae and Arachnactidae) and larval zoanthids (Sphenopidae) were made during blackwater SCUBA dives off Palm Beach, Florida, USA, and off Punaauia, Tahiti, French Polynesia. We report and illustrate the behaviour of these interactions, and suggest an advantage for the anthozoans.},
}

@article {pmid40908282,
year = {2025},
author = {Nishida, H and Itakura, M and Win, KT and Li, F and Kakizaki, K and Suzuki, A and Ohkubo, S and Duc, LV and Sugawara, M and Takahashi, K and Shenton, M and Masuda, S and Shibata, A and Shirasu, K and Fujisawa, Y and Tsubokura, M and Akiyama, H and Shimoda, Y and Minamisawa, K and Imaizumi-Anraku, H},
title = {Genetic design of soybean hosts and bradyrhizobial endosymbionts reduces N2O emissions from soybean rhizosphere.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8023},
pmid = {40908282},
issn = {2041-1723},
support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; },
mesh = {*Glycine max/genetics/microbiology/metabolism ; *Symbiosis/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Bradyrhizobium/genetics/physiology ; Nitrogen Fixation ; Soil Microbiology ; Rhizobium/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Soybeans fix atmospheric N2 through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N2O)-reducing (N2OR) activities, can be leveraged to reduce N2O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N2OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N2OR activity predominantly infect. Our optimize symbiotic system substantially reduces N2O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices.},
}

*Glycine max/genetics/microbiology/metabolism
*Symbiosis/genetics
*Nitrous Oxide/metabolism
*Rhizosphere
*Bradyrhizobium/genetics/physiology
Nitrogen Fixation
Soil Microbiology
Rhizobium/genetics
Bacterial Proteins/genetics/metabolism

@article {pmid40906400,
year = {2025},
author = {Zeng, Q and Wang, Z and Shen, Z and Li, W and Luo, K and Qin, Q and Li, S and Gu, Q},
title = {Microbiome Diversity and Dynamics in Lotus-Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081092},
pmid = {40906400},
issn = {2079-7737},
support = {2023YFD2400902//National Key Research and Development Program of China/ ; 2023YFD2401605//National Key Research and Development Plan Program/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; },
abstract = {The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.},
}

@article {pmid40906396,
year = {2025},
author = {Makwarela, TG and Seoraj-Pillai, N and Nangammbi, TC},
title = {Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081086},
pmid = {40906396},
issn = {2079-7737},
abstract = {Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host's genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk-microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science.},
}

@article {pmid40906361,
year = {2025},
author = {Alcantar-Orozco, EJ and Hernández-Elizárraga, VH and Vega-Tamayo, JE and Ibarra-Alvarado, C and Caballero-Pérez, J and Rodríguez de San Miguel, E and Rojas-Molina, A},
title = {Comparative Proteomic Analysis of Non-Bleached and Bleached Fragments of the Hydrocoral Millepora complanata Reveals Stress Response Signatures Following the 2015-2016 ENSO Event in the Mexican Caribbean.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081042},
pmid = {40906361},
issn = {2079-7737},
abstract = {The hydrocoral Millepora complanata (fire coral) plays a critical role in reef structure and relies on a symbiotic relationship with Symbiodiniaceae algae. Environmental stressors derived from climate change, such as UV radiation and elevated temperatures, disrupt this symbiosis, leading to bleaching and threatening reef survival. To gain insight into the thermal stress response of this reef-building hydrocoral, this study investigates the proteomic response of M. complanata to bleaching during the 2015-2016 El Niño event. Fragments from non-bleached and bleached colonies of the hydrocoral M. complanata were collected from a coral reef in the Mexican Caribbean, and proteomic extracts were analyzed using nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). Uni- and multivariate analyses were applied to identify significant differences in protein abundance. A total of 52 proteins showed differential abundance, including 24 that showed increased expression and 28 whose expression decreased in bleached fragments. Differentially abundant proteins were associated with amino acid biosynthesis, carbohydrate metabolism, cytoskeleton organization, DNA repair, extracellular matrix composition, redox homeostasis, and protein modification. These molecular alterations reflect critical physiological adaptations that may influence stress sensitivity or tolerance in hydrocorals. The findings indicate that heat stress induces molecular responses involving protein refolding, enhanced vesicular transport, cytoskeletal reorganization, and modulation of redox activity. This contributes to a deeper understanding of the molecular mechanisms underlying bleaching in reef-building hydrozoans and broadens current knowledge beyond the more extensively studied anthozoan corals.},
}

@article {pmid40906247,
year = {2025},
author = {Mohamed, HI and Ullah, I and Toor, MD and Tanveer, NA and Din, MMU and Basit, A and Sultan, Y and Muhammad, M and Rehman, MU},
title = {Heavy metals toxicity in plants: understanding mechanisms and developing coping strategies for remediation: a review.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {95},
pmid = {40906247},
issn = {2197-4365},
abstract = {Heavy metal (HM) contamination is an increasing environmental and agricultural concern due to the persistence, toxicity, and bioaccumulative nature of metals such as cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As). These pollutants are primarily introduced through industrial effluents, mining, and agrochemicals, negatively impacting soil health, crop productivity, and food safety, ultimately posing serious risks to both ecosystems and human health. Conventional remediation methods can be costly, labor-intensive, and environmentally disruptive. Heavy metals like Cd, Pb, Hg, and As disrupt cellular homeostasis, inhibit photosynthesis, generate oxidative stress, and interfere with nutrient uptake, leading to significant yield losses in plants. In response to these stresses, plants utilize complex molecular mechanisms for tolerance, including the activation of antioxidant enzymes, upregulation of metal transporters, production of metal-chelating molecules, and modulation of stress-responsive genes and transcription factors. In contrast, bioremediation offers a sustainable and eco-friendly alternative by leveraging the detoxification capabilities of plants, microbes, and their symbiotic interactions. Techniques such as phytoremediation, microbial-assisted remediation, and integrated strategies involving biochar and organic amendments have demonstrated promising results in restoring heavy metal-contaminated soils. Recent advancements in molecular biology and synthetic biology have further improved the efficiency of bioremediation through the genetic engineering of hyperaccumulator plant species and metal-resistant microbes. This review examines the toxic effects of heavy metals on plants and highlights innovative, nature-based remediation strategies, emphasizing their potential for scalable and sustainable environmental cleanup.},
}

@article {pmid40906125,
year = {2025},
author = {Basit, A and Haq, IU and Hyder, M and Humza, M and Younas, M and Akhtar, MR and Ghafar, MA and Liu, TX and Hou, Y},
title = {Microbial Symbiosis in Lepidoptera: Analyzing the Gut Microbiota for Sustainable Pest Management.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080937},
pmid = {40906125},
issn = {2079-7737},
support = {National Natural Science Foundation of China (U22A20489; 32361143791).//National Natural Science Foundation of China (U22A20489; 32361143791)./ ; },
abstract = {Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms-including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia-that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future.},
}

@article {pmid40906110,
year = {2025},
author = {Meesil, W and Ardpairin, J and Sharkey, LKR and Pidot, SJ and Vitta, A and Thanwisai, A},
title = {Whole-Genome Sequencing and Biosynthetic Gene Cluster Analysis of Novel Entomopathogenic Bacteria Xenorhabdus thailandensis ALN 7.1 and ALN 11.5.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080905},
pmid = {40906110},
issn = {2079-7737},
support = {PHD / 0084/2561//Royal Golden Jubilee Ph.D. Program/ ; R2566B043//Naresuan University (NU) and the National Science, Research and Innovation Fund (NSRF)/ ; R2567C003//Global and Frontier Research University Fund, Naresuan University/ ; },
abstract = {Xenorhabdus species are entomopathogenic bacteria that live in symbiosis with Steinernema nematodes and produce a wide range of bioactive secondary metabolites. This study aimed to characterize the complete genomes and biosynthetic potential of two novel Xenorhabdus isolates, ALN7.1 and ALN11.5, recovered from Steinernema lamjungense collected in Northern Thailand. High-quality genome assemblies were generated, and phylogenomic comparisons confirmed that both isolates belonged to the recently described species Xenorhabdus thailandensis. The assembled genomes were approximately 4.02 Mb in size, each comprising a single circular chromosome with a GC content of 44.6% and encoding ~3800 protein-coding sequences, consistent with the features observed in other members of the genus. Biosynthetic gene cluster (BGCs) prediction using antiSMASH identified 19 BGCs in ALN7.1 and 18 in ALN11.5, including known clusters for holomycin, pyrrolizixenamide, hydrogen cyanide, and gamexpeptide C, along with several uncharacterized clusters, suggesting unexplored metabolic potential. Comparative analyses highlighted conserved yet strain-specific BGC profiles, indicating possible diversification within the species. These results provide genomic insights into X. thailandensis ALN7.1 and ALN11.5 and support their potential as valuable sources for the discovery of novel natural products and for future biotechnological applications.},
}

@article {pmid40906071,
year = {2025},
author = {Zeng, X and Chen, J and Liu, G and Zhou, Y and Wang, L and Zhang, Y and Liu, S and Shao, Z},
title = {Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080954},
pmid = {40906071},
issn = {2079-7737},
support = {2023YFC2812903, 2021YFF0501304, and 2018YFC0310702.//National Key R&D Program of China/ ; },
abstract = {Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14-0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin-Benson-Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32-4.60). Its black variety scales were dominated by Campylobacterota (67.01-80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order "Endothiobacterales," were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin-Benson-Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails' adaptation to vent ecosystems.},
}

@article {pmid40904995,
year = {2025},
author = {Haque, MT and Paul, S and Herberstein, ME and Khan, MK},
title = {A parasitic or mutualistic conundrum: can symbiotic protists increase thermal tolerance in a semi-aquatic insect?.},
journal = {Royal Society open science},
volume = {12},
number = {9},
pages = {251061},
pmid = {40904995},
issn = {2054-5703},
abstract = {Rising temperatures and frequent heatwaves pose a major threat to ectotherms due to their reliance on environmental temperature for physiological processes. Thermal tolerance, the ability to withstand varying temperature, determines how effectively and efficiently individuals can survive under extreme conditions. Host-microbial symbiotic interactions can influence thermal tolerance in insects; however, we have limited information especially for some endosymbionts such as gregarines, a group of apicomplexan endoparasites, which are commonly found in the guts of many aquatic and terrestrial insects. Gregarines are often considered parasitic, while a few recent studies have shown beneficial effects on hosts. Here, we tested the impact of gregarines on thermal tolerance in Ischnura heterosticta damselflies. We found that damselflies naturally infected with gregarines had higher thermal tolerance than damselflies without gregarine infections. Our findings provide evidence in support of gregarines as an endosymbiont of I. heterosticta damselfly. Our study indicates that gregarine endosymbionts may assist damselfly and possibly other semi-aquatic insects to sustain extreme heat and highlights the importance of understanding host-symbiont interactions in the context of climate change and species conservation.},
}

@article {pmid40904700,
year = {2025},
author = {Wei, G and Li, B and Huang, M and Lv, M and Liang, Z and Zhu, C and Ge, L and Chen, J},
title = {Polarization of Tumor Cells and Tumor-Associated Macrophages: Molecular Mechanisms and Therapeutic Targets.},
journal = {MedComm},
volume = {6},
number = {9},
pages = {e70372},
pmid = {40904700},
issn = {2688-2663},
abstract = {Tumor-associated macrophages (TAMs) are prominent constituents of solid tumors, and their prevalence is often associated with poor clinical outcomes. These highly adaptable immune cells undergo dynamic functional changes within the immunosuppressive tumor microenvironment (TME), engaging in reciprocal interactions with malignant cells. This bidirectional communication facilitates concurrent phenotypic transformation: tumor cells shift toward invasive mesenchymal states, whereas TAMs develop immunosuppressive, pro-tumorigenic traits. Increasing evidence highlights metabolic reprogramming, characterized by dysregulation of lipid metabolism, amino acid utilization, and glycolytic activity, as the fundamental molecular basis orchestrating this pathological symbiosis. However, a comprehensive understanding of how metabolic reprogramming specifically coordinates the mutual polarization of tumor cells and TAMs is lacking. This review thoroughly examines the molecular mechanisms governing this co-polarization process, detailing critical transcriptional regulators, essential signaling pathways, and the maintenance of adaptive phenotypes within the TME. Furthermore, this review critically assesses promising therapeutic strategies aimed at disrupting this alliance, including the use of metabolically targeted agents, engineered chimeric antigen receptor macrophages, and TAM-selective nanoparticle delivery systems. These insights provide a crucial foundation for the development of next-generation cancer immunotherapies focused on reprogramming pathological polarization dynamics to overcome treatment resistance and improve clinical outcomes.},
}

@article {pmid40904148,
year = {2025},
author = {Liu, JJ and Yu, QX and Chen, DH and Wu, LS and Si, JP},
title = {[Research progress in key technologies for the development of Dendrobium officinale: from a rare and endangered species to a 10-billion-RMB-level industry].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {13},
pages = {3670-3678},
doi = {10.19540/j.cnki.cjcmm.20250508.103},
pmid = {40904148},
issn = {1001-5302},
mesh = {*Dendrobium/growth & development/microbiology ; Endangered Species ; Seeds/growth & development/microbiology ; Fungi/physiology ; },
abstract = {Dendrobium officinale(DO) is a traditional Chinese medicinal and edible plant, while it is critically endangered worldwide. This article, primarily based on the original research findings of the author's team and available articles, provides a comprehensive overview of the factors contributing to the endangerment of DO and the key technologies for the conservation, efficient cultivation, and value-added utilization of this plant. The scarcity of wild populations, low seed-setting rates, lack of endosperm in seeds, and the need for symbiosis with endophytic fungi for seed germination under natural conditions are identified as the primary causes for the rarity and endangerment of DO. Artificial seed production and tissue culture are highlighted as key technologies for alleviating the endangered status. The physiological and ecological mechanisms underlying the adaptation of DO to epiphytic growth are explored, and it is proposed that breaking the coupling of high temperature and high humidity is essential for preventing southern blight, a devastating affliction of DO. The roles of endophytic fungi in promoting the growth, improving the quality, and enhancing the stress resistance of DO are discussed. Furthermore, the integration of variety breeding, environment selection, and co-culture with endophytic fungi is emphasized as a crucial approach for efficient cultivation. The value-added applications of DO in pharmaceuticals, health foods, food products, and daily chemicals-particularly in the food and daily chemical industries-are presented as key drivers for a 10-billion-RMB-level industry. This systematic review offers valuable insights for the further development, utilization, and industrialization of DO resources, as well as for the broader application of conservation strategies for other rare and endangered plant species.},
}

*Dendrobium/growth & development/microbiology
Endangered Species
Seeds/growth & development/microbiology
Fungi/physiology

@article {pmid40904135,
year = {2025},
author = {Guo, BL and Pan, C},
title = {[Resource assessment as collaborative bridge: resolving dilemmas and fostering symbiosis in traditional Chinese medicine research and industry].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {13},
pages = {3556-3560},
doi = {10.19540/j.cnki.cjcmm.20250508.102},
pmid = {40904135},
issn = {1001-5302},
mesh = {*Medicine, Chinese Traditional ; Quality Control ; *Drugs, Chinese Herbal/standards/economics ; Humans ; *Drug Industry ; Symbiosis ; },
abstract = {The research and development of new traditional Chinese medicine(TCM) drugs has entered a phase integrating high-quality development with resource assurance. Drawing from 18 new TCM drug registration resource assessment projects, this study systematically summarizes three core challenges in TCM resource management:(1) industrial chain complexity amplifies quantity-quality risks through material heterogeneity(multi-origin variations and wild-to-cultivated genetic shifts) and production chain coupling(germplasm-cultivation-processing whole-chain volatility);(2) structural misalignment among institutions, enterprises, and producers leads to disattachment of research and development from industrial demand;(3) technical barriers exist in quality control systems, involving producing area shift, cultivation evolution, and harvesting and processing innovations. This study proposes a four-dimensional assessment framework prioritizing "species stabilization, quantity availability, quality control, and quality optimization", which is supported by an early-warning system addressing multi-origin selection, adulterant control, endangered species protection, and standardized cultivation. Risk management strategies emphasize supply chain traceability, particularly for imported and ethnic medicinal materials. Using Epimedii Folium as a case study, this study demonstrates a tripartite industrial upgrade paradigm integrating premium germplasm, cultivation technology, and quality control, ultimately establishing an innovation mechanism with deep academia-industry collaboration. The research advocates transforming resource assessment from compliance checks to strategic decision-making tools through enhanced academia-industry collaboration, so as to provide resource assurance for high-quality TCM development.},
}

*Medicine, Chinese Traditional
Quality Control
*Drugs, Chinese Herbal/standards/economics
Humans
*Drug Industry
Symbiosis

@article {pmid40903900,
year = {2025},
author = {Yuan, QS and Luo, L and Shi, H and Wang, H and An, J and Gao, Y and Xu, J and Ou, X and Yang, Y and Tabl, KM and Guo, L and Huang, L and Zhou, T},
title = {Fungal symbiont Mycena complements impaired nitrogen utilization in Gastrodia elata and supplies indole-3-acetic acid to facilitate its seed germination.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101500},
doi = {10.1016/j.xplc.2025.101500},
pmid = {40903900},
issn = {2590-3462},
abstract = {Nitrogen and auxin uptake plays pivotal roles in seed germination and development. Gastrodia elata, a fully mycoheterotrophic plant, depends entirely on its symbiotic association with Mycena for early growth and seed germination. The process by which Mycena enables the supply of nitrogen nutrients and auxin, which are deficient in G. elata, remains poorly understood. In this study, a genome-scale dataset for G. elata revealed the loss of genes associated with nitrogen utilization and indole-3-acetic acid (IAA) biosynthesis, genes which were present in Mycena. Further evaluation of the dynamic transcriptomic interactions between G. elata seeds and Mycena at different symbiotic stages demonstrated that genes involved in nitrogen- and tryptophan-dependent IAA biosynthesis were significantly upregulated in Mycena. Concurrently, G. elata seeds exhibited increased expression of genes involved in the "hormone signal transduction pathway" and "starch and sucrose metabolism pathway." As representative enzymes in nitrogen assimilation and IAA biosynthesis pathways, functional disruption of nitrite reductase (MyNir, EVM0012344) and amidase (MyAmid, EVM0010270) in Mycena significantly impeded the symbiotic germination of G. elata seeds. This disruption interfered with the energy supply and caused cellular restructuring and hormonal signaling crosstalk. In conclusion, our findings provide novel insights into the mutualistic symbiotic relationship between Mycena and G. elata. Specifically, the fungus Mycena compensated for the incomplete nitrogen metabolism of its plant partner, G. elata, promoting seed germination. These results shed light on plant-fungal symbiotic associations from the perspective of nitrogen utilization.},
}

@article {pmid40900337,
year = {2025},
author = {Liu, J and Du, C and Xu, N and Shi, C and Liu, B and Tu, B and Zhang, K and Gao, K},
title = {A novel algae-assisted sequencing batch and intermittent air-lift bioreactor (A-SBIAB) using polyester filament-based carriers for piggery wastewater treatment.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {40900337},
issn = {1615-7605},
abstract = {Algae-assisted biological wastewater treatment technology has been widely applied in wastewater treatment due to its low cost and great removal performance. However, the stabilization and sustainability of the alga-bacteria symbiosis system still need to be developed. In this work, an algae-assisted sequencing batch and intermittent air-lift bioreactor (A-SBIAB) system was constructed for removing the nutrients from the piggery wastewater. A strengthened algae-bacterial symbiosis system was also achieved with the aid of a suspended bio-carrier composed of polyester filament fixed on concentric plastic rings, which provided enhanced surface area and illumination access for microbial attachment. The removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) were up to 92.0%, 81.7% and 89.3%, respectively, at the optimum parameters (Chl-a concentration of 1000 mg/m[3], light intensity of 6000 lx and lighting time 10 h). The Campylobacteria (72.05%), Desulfuromonadia (11.16%), Spirochaetia (3.10%) and Bacteroidia (1.73%) as the dominant bacterial communities would be responsible for the nitrate ammonification, nitrogen fixation, nitrate reduction and organics degradation, respectively. Meanwhile, Chlorophyceae (98.21%) became the overwhelming algal community, playing a positive effect on the nutrients removal.},
}

@article {pmid40898710,
year = {2025},
author = {Laplanche, V and Speciale, I and De Castro, C and Juge, N},
title = {Cell surface polysaccharides in the gut microbiota: occurrence, structure and role.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2536082},
doi = {10.1080/19490976.2025.2536082},
pmid = {40898710},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Polysaccharides, Bacterial/chemistry/metabolism ; *Bacteria/chemistry/metabolism/genetics/classification ; *Gastrointestinal Tract/microbiology ; Animals ; Cell Wall/chemistry/metabolism ; Symbiosis ; *Polysaccharides/chemistry/metabolism ; Host Microbial Interactions ; },
abstract = {The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and immune cells through effector molecules secreted or attached to the cell surface. Although cell surface polysaccharides have mainly been studied in the context of pathogen-host interactions, these are increasingly being recognized as important factors of the symbiotic interaction between the gut microbiota and the host conferring biological activities and physiological functions. In this review, we focus on the structure and role of polysaccharides surrounding the bacterial cell wall, namely capsular polysaccharide (CPS) and cell wall polysaccharides (CWPS), both tightly linked to the cell surface, and exopolysaccharides (EPS) which are loosely attached to the extracellular surface or secreted into the environment. We will focus on structurally characterized CPS, CWPS and EPS from both gut commensal bacteria and food-derived bacteria found in the gut. These polysaccharides show high structural diversity and are important for the bacteria to adapt to the GI environment and/or influence host immune response. The combined diversity of microbes in the gut provides a vast array of glycans that could be harnessed to benefit human health.},
}

*Gastrointestinal Microbiome
Humans
*Polysaccharides, Bacterial/chemistry/metabolism
*Bacteria/chemistry/metabolism/genetics/classification
*Gastrointestinal Tract/microbiology
Animals
Cell Wall/chemistry/metabolism
Symbiosis
*Polysaccharides/chemistry/metabolism
Host Microbial Interactions

@article {pmid40898197,
year = {2025},
author = {Kamyab, A and Samsampour, D},
title = {How thyme thrives under drought: insights into photosynthetic and membrane-protective mechanisms.},
journal = {BMC biotechnology},
volume = {25},
number = {1},
pages = {95},
pmid = {40898197},
issn = {1472-6750},
mesh = {*Photosynthesis/physiology ; *Droughts ; *Thymus Plant/physiology/microbiology/metabolism ; Chlorophyll/metabolism ; Ferric Compounds/pharmacology/chemistry ; Endophytes/physiology ; },
abstract = {BACKGROUND: Drought is an abiotic stress that significantly reduces the yield of thyme (Thymus vulgaris). This study investigated how iron oxide nanoparticles (FeNPs), together with symbiotic bacterial (Azospirillum lipoferum) and fungal (Aspergillus oryzae) endophytes, modulate osmotic adjustment, molecular and biochemical mechanisms related to photosynthesis, and drought tolerance mechanisms in thyme.

RESULTS: The experiment was evaluated as a factorial experiment in a completely randomized design with three replications. evaluating three treatment factors: four irrigation levels (100%, 75%, 50%, and 25% of field capacity), four FeNPs concentrations (0, 0.5, 1, and 1.5 mg L⁻¹), and three endophyte treatments (control, bacterial (EB), and fungal (EF) inoculation). At 25% FC, EB and spraying with 1 mg L[- 1] FeNPs increased Fv/Fm (maximum quantum efficiency of photosystem II), chlorophyll a, chlorophyll b, and total chlorophyll, carotenoids, relative water content (RWC), and protein levels level protein levels by 18.75%, 10.41%, 31.54%, 18.20%, 14.26%, 35.53%, and 125.22% respectively, compared to the control. At 25% FC, electrolyte leakage (EL) was increased by 47.44% with the combination of EF and 1.5 mg L[- 1] FeNPs. The highest proline accumulation at 25% FC was observed after inoculation with EF and 1 mg L[- 1] FeNPs, resulting in significant increases of 36.36% and 13.04%, respectively, compared to the control. Soluble sugar was remarkably increased by 28.57% under upon treatment with FeNPs (1.5 mg L[- 1] FeNPs). At 25% FC, EB and 1.5 mg L[- 1] FeNPs showed significant reductions of 17.33% and 37.10%, respectively, in malondialdehyde levels compared to control plants. At 50% FC, 1 mg L⁻¹ FeNPs increased Catalase by 15%, peroxidase by 31.25%, and superoxide dismutase by 43.42%, while higher concentrations reduced enzyme activities. Similarly, 1.5 mg L⁻¹ FeNPs and EB inoculation enhanced ascorbate peroxidase by 37.44% and 17.37%, respectively. FeNPs acted as abiotic stressors at low levels but became toxic at higher concentrations.

CONCLUSION: Our findings demonstrate that the synergistic application of FeNPs and endophytes significantly enhances drought tolerance in T. vulgaris by optimizing photosynthetic efficiency (Fv/Fm, chlorophyll content) and preserving membrane integrity (RWC, MDA reduction). These results provide a framework for leveraging nano-bio partnerships to improve crop resilience under water scarcity.},
}

*Photosynthesis/physiology
*Droughts
*Thymus Plant/physiology/microbiology/metabolism
Chlorophyll/metabolism
Ferric Compounds/pharmacology/chemistry
Endophytes/physiology

@article {pmid40894865,
year = {2025},
author = {Masoudi, A and Joseph, RA and Keyhani, NO},
title = {Spatial organization within social ambrosia beetle nests limits spread of infectious disease.},
journal = {iScience},
volume = {28},
number = {9},
pages = {113281},
doi = {10.1016/j.isci.2025.113281},
pmid = {40894865},
issn = {2589-0042},
abstract = {Ambrosia beetles are social, fungal-farming insects that nest within tree xylem. Their close living conditions make them potentially vulnerable to microbial infectious diseases. We show that the insect pathogenic fungus Metarhizium anisopliae effectively infects and kills Xyleborus affinis adults, even within sawdust-based colony habitats. Healthy beetles did not avoid infected nestmates, and increased contact led to higher mortality and reduced offspring; however, larvae and pupae were still produced, even when colonies began with only infected beetles. Diseased individuals and Metarhizium CFUs were concentrated in the upper third of the nest, while surviving adults and brood were found in the middle/lower areas. A beetle symbiotic fungus, Neocosmospora sp. Xa1 was identified, which inhibited Metarhizium growth, potentially aiding in defense. Our findings suggest spatial structuring and microbial interactions within the nest help protect vulnerable brood to support colony persistence, revealing colony-level mechanisms that buffer against spread of infectious diseases, favoring offspring survival.},
}

@article {pmid40894719,
year = {2025},
author = {De Santiago, A and Barnes, S and Pereira, TJ and Marcellino-Barros, M and Durden, L and Han, MK and Thrash, JC and Bik, HM},
title = {Pseudoalteromonas is a novel symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.22.671635},
pmid = {40894719},
issn = {2692-8205},
abstract = {Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided mixed results when evaluating patterns of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, an overlooked bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a novel symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g., Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with FISH images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional mutualisms. In marine environments, we hypothesize that horizontally-acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with Vitamin B, amino acids, and bioavailable carbon compounds in return.},
}

@article {pmid40894499,
year = {2025},
author = {Liu, Z and Zhao, X and Yang, J and Chen, X and Cai, Y and Shaaban, M and Peng, QA and Cai, Y},
title = {Microbial removal mechanism of chromium and cadmium by humic acid-loaded nano zero-valent iron prepared by liquid-phase reduction method.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1596063},
doi = {10.3389/fpls.2025.1596063},
pmid = {40894499},
issn = {1664-462X},
abstract = {Heavy metal pollution is a global issue that has drawn significant attention due to its environmental and health risks. This thesis focuses on the research of highly toxic chromium and cadmium in the environment. It explores the removal mechanism of Cr and Cd contamination using humic acid-loaded nano-zero-valent iron (NZVI@HA) prepared through a liquid-phase reduction method. Additionally, it investigates the interaction mechanism of removing Cr and Cd contamination by synergizing with the Chromium and Cadmium Symbiotic Bacterial Colony (NZVI@HA+Cr/CdMC). The findings indicate that NZVI@HA exhibited optimal removal efficiency for Cr(VI) at pH=2 (85.7%) and Cd(II) at pH=8 (94.8%). The initial concentration of Cr and Cd pollution showed an inverse relationship with the removal rates of Cd(II) and Cr(VI). Moreover, the reaction temperatures were positively correlated with the removal rates of Cd(II) and Cr(VI). Cu2+ significantly enhanced Cr(VI) removal in the water column (p<0.01), whereas Zn2+ notably inhibited Cd(II) removal (p<0.05). In the NZVI@HA+Cr/CdMC system, extracellular polymers (EPS), tyrosine, and tryptophan, through van der Waals forces, facilitated the removal of Cd(II) and Cr(VI) complexation. This reduced the stress of Cr(VI) and Cd(II) on Cr/CdMC, thereby enhancing the removal of Cr(VI) and Cd(II).},
}

@article {pmid40894109,
year = {2025},
author = {Lopez, JV and Pomponi, SA and Hentschel, U and Erpenbeck, D and Pruzinsky, N and Fiore, C and Mulheron, R and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {336},
doi = {10.12688/wellcomeopenres.24173.1},
pmid = {40894109},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Xestospongia muta (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including Candidatus Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.},
}

@article {pmid40894070,
year = {2025},
author = {Tayeh, M and Sama-Ae, I and Wisessombat, S and Sianglum, W},
title = {Antimigration and Anti-Invasion Properties of Aspergillus aculeatus Extract, an Endophyte Isolated From Capsicum annuum L. on Non-Small-Cell Lung Cancer Cells: In Vitro Experiments and In Silico Methods.},
journal = {Scientifica},
volume = {2025},
number = {},
pages = {5676577},
doi = {10.1155/sci5/5676577},
pmid = {40894070},
issn = {2090-908X},
abstract = {Endophytic fungi are microorganisms that infect living plant tissues internally without producing obvious symptoms of infection, existing in a symbiotic relationship with plants for a portion of their life cycle. Currently, endophytic fungi serve as alternate sources for the production of new bioactive chemicals with great efficacy. This study aimed to examine the antimigration and anti-invasion capabilities of the endophytic fungus Aspergillus aculeatus extract, isolated from Capsicum annuum L., utilizing in vitro and in silico methods. This study isolated the endophytic fungus A. aculeatus from the leaves of C. annuum L. LC-MS analysis revealed fifty-five active components within the extract. Ten compounds exhibited favorable results in the in silico assessment. Computational predictions indicate that tajixanthone methanoate (-8.80 kcal/mol) and aspernigerin (-12.95 kcal/mol) exhibited high binding affinity against MMP-2. The A. aculeatus extract demonstrated antiproliferative activity with an IC50 value of 286.36 ± 122.57 μg/mL. The extract, at noncytotoxic concentrations, reduced the migration and invasion of A549 cells in a dose-dependent manner. Furthermore, A. aculeatus extract demonstrated a marked reduction in MMP-2 activity. According to these results, the compounds may serve as antimigration and anti-invasion agents by inhibiting the MMP-2 protein. The results demonstrated that A. aculeatus extract derived from C. annuum L. inhibited A549 cell migration and invasion via reducing MMP-2 activity. The findings indicated that A. aculeatus extract derived from C. annuum L. may be utilized for the treatment of lung cancer.},
}

@article {pmid40893913,
year = {2025},
author = {Pandit, SS and Meganathan, P and Vedagiri, H},
title = {Harmonizing gut microbiota dysbiosis: Unveiling the influence of diet and lifestyle interventions.},
journal = {Metabolism open},
volume = {27},
number = {},
pages = {100384},
doi = {10.1016/j.metop.2025.100384},
pmid = {40893913},
issn = {2589-9368},
abstract = {The gut microbiota, comprising trillions of microorganisms inhabiting the gastrointestinal tract, is essential to human health and disease. Recent research has illuminated the interactions between many components of human physiology and the gut microbiota, including immune function, metabolism, and neurological health. Central to maintaining this symbiotic relationship is the concept of dysbiosis - an imbalance in the makeup and roles of the gut microbiota. Dysbiosis of the gut microbiota has emerged as a significant factor in the pathogenesis of numerous health conditions, spanning from gastrointestinal disorders like inflammatory bowel disease and irritable bowel syndrome to systemic diseases such as obesity, metabolic syndrome, and even neurological disorders like depression and anxiety. While dysbiosis can result from a myriad of factors including antibiotic use, stress, and genetic predispositions, emerging evidence suggests that diet and lifestyle choices exert profound influences regarding the make-up and capabilities of the gut microbiota. In this review, We explore the complex interactions among lifestyle, nutrition, and gut microbial dysbiosis. In particular, we investigate how the gut microbiota can be modified and dysbiosis can be mitigated by dietary patterns, food composition, prebiotics, probiotics, and lifestyle factors including exercise, stress reduction, and good sleep hygiene. Restoring microbial balance and enhancing general health and well-being can be achieved through preventive and therapeutic measures that can be made more effective by understanding how dietary and lifestyle changes might affect the gut microbiota. Through this exploration, we aim to elucidate the possibility of using lifestyle and dietary modifications as tools for managing gut microbial dysbiosis.},
}

@article {pmid40893412,
year = {2025},
author = {Margarita, V and Nguyen, THT and Petretto, GL and Congiargiu, A and Ligas, A and Diaz, N and Ton Nu, PA and Pintore, G and Rappelli, P},
title = {Effect of essential oils from Cymbopogon citratus, Citrus grandis, and Mentha arvensis on Trichomonas vaginalis and role of its symbionts Mycoplasma hominis and Ca. Mycoplasma girerdii.},
journal = {Frontiers in parasitology},
volume = {4},
number = {},
pages = {1610965},
doi = {10.3389/fpara.2025.1610965},
pmid = {40893412},
issn = {2813-2424},
abstract = {INTRODUCTION: Trichomoniasis, the most common non-viral sexually transmitted disease, is caused by the protozoon Trichomonas vaginalis. T. vaginalis can establish a symbiosis with two bacteria, Mycoplasma hominis and Candidatus Mycoplasma girerdii, whose intracellular presence may modulate several characteristics of the protozoan, including its sensitivity to 5-nitroimidazoles, the only class of drugs currently effective in treating trichomoniasis. The rising prevalence of T.vaginalis strains resistant to metronidazole, the most commonly used antitrichomonal drug, underscores the need for therapeutic alternatives active against the protozoon.

METHODS: In this study, we evaluate the antimicrobial activity of essential oils extracted from three plants cultivated in Vietnam - Cymbopogon citratus, Citrus grandis, and Mentha arvensis - against thirty T. vaginalis strains isolated from symptomatic women in Italy and Vietnam. We also assess the influence of M. hominis and Ca. M. girerdii on T. vaginalis susceptibility to essential oils and metronidazole, through dedicated susceptibility assays. Additionally, given the importance of lactobacilli in maintaining vaginal health, we investigate the effects of the essential oils on Lactobacillus gasseri and Lactobacillus crispatus. The cytotoxic activity of the oils against HeLa cells was also tested in vitro.

RESULTS: All three essential oils showed effective antitrichomonal activity without inhibiting lactobacilli growth. Among them, C. citratus oil exhibited the strongest inhibitory effect on T. vaginalis, including strains harboring bacterial symbionts. Moreover, the oils demonstrated no cytotoxic activity against HeLa cells at the concentrations effective against the protozoan.

DISCUSSION: The results support the potential of C. citratus essential oil as a natural antitrichomonal agent. Its effectiveness against both free and symbiont-infected T. vaginalis strains positions it as a promising candidate for developing alternative therapies against drug-resistant trichomoniasis.},
}

@article {pmid40891805,
year = {2025},
author = {Cheng, P and Wang, Z and Lu, B and Zhao, Y and Zhang, H},
title = {Effect of different concentrations of gibberellins on antibiotics and nutrient removal using microalgae-bacteria consortia system.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/15226514.2025.2554172},
pmid = {40891805},
issn = {1549-7879},
abstract = {Phytohormone gibberellins (GAs) were utilized to enhance the removal of tetracycline antibiotics and nutrients from swine wastewater by different algal-bacterial symbiosis. Compared to microalgae monoculture, microalgae-activated sludge, and microalgae-Bacillus licheniformis, microalgae-endophytic bacteria showed better growth, photosynthetic, and purification performance. At 50 mg L[-1] GAs addition concentration, the specific growth rate of Chlorella vulgaris-endophytic bacterial (S395-2) system was 0.331 ± 0.03 d[-1], the maximum removal rate of tetracycline (TC), total nitrogen (TN) and total phosphorus (TP) was 96.31 ± 2.73%, 86.37 ± 8.31% and 87.26 ± 8.42%, respectively. The purification effect was much higher than the level of microalgae monoculture without GAs addition (TC removal of 81.33 ± 7.71%, TN and TP removal of 62.51 ± 5.95% and 64.25 ± 6.13%, respectively). In summary, exogenous GAs simultaneously promoted the resistance and biomass accumulation of algal symbiosis, which supplied a theoretical foundation for the treatment of high-concentration nutrients and antibiotics wastewater.},
}

@article {pmid40891513,
year = {2025},
author = {McCauley, M and Montesanto, F and Bedgood, SA and Miner, C and Plichon, K and Weis, VM and Loesgen, S},
title = {Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf189},
pmid = {40891513},
issn = {1751-7370},
abstract = {Symbiodiniaceae-associated microbiota strongly affect cnidarian symbioses. We systematically reduced the bacterial and fungal communities associated with Symbiodiniaceae to study effects on the cnidarian holobiont Exaiptasia diaphana (Aiptasia). Clonal anemones were inoculated with xenic Breviolum minutum (SSB01) and microbiome manipulated cultures after antibacterial or antifungal treatment. The asexual reproduction of pedal laceration allowed for three generations of clonal aposymbiotic Aiptasia to be included in this study, from the initial adult generation (G0), to the first (G1) and second (G2) generation. We inoculated small and large G1 Aiptasia with algae and monitored onset of symbiosis, rate of algal proliferation, and holobiont characteristics. Sequencing the 16S and 18S rRNA gene regions identified significant differences in the bacterial and fungal communities of the G0 and G1 generations, alongside differences between the size classes of small and large G1 anemones. The microbiome of larger G1 individuals was distinct to the smaller G1 anemones, suggesting a microbiome maturation process. Control B. minutum cultures exhibited a significantly greater proliferation rate in large G1 anemones when compared to antibacterial or antifungal treated cultures, whereas the opposite trend was documented in the small G1 anemones. Although no differences were observed between algal photochemical parameters, or the growth and behavior of G1 juveniles, we observed a significant influence in the production of G2 clones between treatments. Overall, we provide strong ecological implications of manipulating Symbiodiniaceae microbiome, not for the algae themselves, but for the maturation of the host Aiptasia, as well as for the cnidarian holobiont over multiple generations.},
}

@article {pmid40891201,
year = {2025},
author = {Zhou, G and Ding, M and Li, X and Jiang, S and Xia, Z and Xie, C and Zhang, W and Wan, Y},
title = {Genome Assembly of Elysia leucolegnote Reveals the Secrets of Autonomous Photosynthesis and Extraordinary Symbiotic Relationships in Photosynthetic Animals.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70155},
pmid = {40891201},
issn = {1365-3040},
support = {//This study is supported by Hainan Normal University Talent Research Start-up Fund Project Funding (HSZK-KYQD-202436)./ ; },
}

@article {pmid40891179,
year = {2025},
author = {Orosz, J and Lin, EX and Torres Ascurra, YC and Kappes, M and Lindsay, P and Bashyal, S and Everett, H and Gautam, CK and Jackson, D and Müller, LM},
title = {CORYNE modulates Medicago truncatula inflorescence meristem branching and plays a conserved role in the regulation of arbuscular mycorrhizal symbiosis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf386},
pmid = {40891179},
issn = {1460-2431},
abstract = {The CLAVATA signaling pathway regulates plant development and plant-environment interactions. CLAVATA signaling consists of mobile, cell-type or environment-specific CLAVATA3/ESR-related (CLE) peptides, which are perceived by a receptor complex consisting of leucine-rich repeat receptor-like kinases such as CLAVATA1 and receptor-like proteins such as CLAVATA2, which often functions with the pseudokinase CORYNE (CRN). CLAVATA signaling has been extensively studied in various plant species for its developmental role in meristem maintenance. In addition, CLAVATA signaling was implicated in plant-microbe interactions, including root nodule symbiosis and plant interactions with mutualistic arbuscular mycorrhizal (AM) fungi. However, knowledge on AM symbiosis regulation by CLAVATA signaling is limited. Here, we report a dual role for Medicago truncatula CRN in development and plant-microbe interactions. In shoots, MtCRN modulates inflorescence meristem branching. In roots, the MtCRN promoter is active in vascular tissues and meristematic regions. In addition, MtCRN expression is activated in cortex cells colonized by AM fungi and negatively regulates root interactions with these microbes in a nitrogen-dependent manner; negative AM symbiosis regulation by CRN was also observed in the monocot Zea mays, suggesting this function is conserved across plant clades. We further report that MtCRN functions partially independently of the AM autoregulation signal MtCLE53. Transcriptomic data revealed that M. truncatula crn roots display signs of perturbed nutrient, symbiosis, and stress signaling, suggesting that MtCRN plays various roles in plant development and interactions with the environment.},
}

@article {pmid40889905,
year = {2025},
author = {Chen, MF and Gao, YZ},
title = {Application of [15]N stable isotope techniques to biological nitrogen fixation in terrestrial ecosystems.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {7},
pages = {1952-1960},
doi = {10.13287/j.1001-9332.202507.010},
pmid = {40889905},
issn = {1001-9332},
mesh = {*Nitrogen Fixation/physiology ; *Nitrogen Isotopes/analysis ; *Ecosystem ; *Isotope Labeling/methods ; Nitrogen/metabolism ; Symbiosis ; },
abstract = {Biological nitrogen fixation (BNF) is an important nitrogen source in terrestrial ecosystems. Accurate estimation of BNF rate is essential to accurately quantify atmospheric nitrogen input to natural ecosystems. [15]N natural abundance is commonly used to measure the BNF in symbiotic and associative nitrogen fixing plants, but are highly dependent on the choice of the reference plants. In contrast, the [15]N isotope labeling technique allows precise determination of BNF rates of symbiotic, free-living, and associative N-fixing types, and surpasses the previous methods in studying plant nitrogen fixation strategies, nitrogen transfer processes, and carbon-nitrogen trading between nodules and hosts. The [15]N isotope dilution method is mainly used for plant nitrogen fixation research. Although the [15]N stable isotope probe technique is technically challenging and expensive, it enables the detection and study of N-fixing microorganisms by labeling DNA or RNA, and provides an effective way for assessing asymbiotic microorganism nitrogen fixation rates. The development of [15]N stable isotope technique provides a strong technical guarantee for biological nitrogen fixation research.},
}

*Nitrogen Fixation/physiology
*Nitrogen Isotopes/analysis
*Ecosystem
*Isotope Labeling/methods
Nitrogen/metabolism
Symbiosis

@article {pmid40888447,
year = {2025},
author = {Petinger, C and Crowley, T and Wyk, BV},
title = {Patterns of Transition of Adolescents in an HIV Care Programme in Peri-Urban Cape Town, South Africa: A Photovoice Study.},
journal = {Journal of the International Association of Providers of AIDS Care},
volume = {24},
number = {},
pages = {23259582251362908},
doi = {10.1177/23259582251362908},
pmid = {40888447},
issn = {2325-9582},
mesh = {Humans ; South Africa/epidemiology ; Adolescent ; *HIV Infections/psychology/therapy/drug therapy ; Male ; Female ; *Transition to Adult Care ; Focus Groups ; Social Support ; Young Adult ; Photography ; Qualitative Research ; Adult ; },
abstract = {Successful transition from paediatric to adult HIV care programme is a critical developmental milestone in the care trajectory of adolescents living with HIV (ALHIV). The transition process involves a shift from a structured, caregiver-supported healthcare model to one that requires independence and self-management. This process should be guided and supportive to ensure continued engagement in care and optimal adherence when ALHIV are transferred. This study utilised photovoice methods to explore the transition experiences of ALHIV in the Cape Town Metropole. Audio-recorded focus group data were transcribed verbatim and subjected to reflexive thematic analysis. Three distinctive patterns of behaviour from ALHIV were identified as themes. Type 1: socially reliant, dependent adolescent who heavily relies on family and peer support and struggles with adherence. Type 2: socially disconnected, hyper-independent adolescent, who is self-reliant, seeks solitude, and is generally resistant to external support. We configured a third (ideal) type, who is interdependent and able to self-manage their chronic condition, but within a supportive health care environment that provides positive healthcare and transition experiences. The findings underscore the need for supportive transition models promoting self-management skills, while facilitating a symbiotic relation with healthcare staff promoting sustained engagement in care well into adulthood. We recommend that adolescent or youth friendly services for ALHIV be expanded to support and monitor the transition process and outcomes in the adult HIV program.},
}

Humans
South Africa/epidemiology
Adolescent
*HIV Infections/psychology/therapy/drug therapy
Male
Female
*Transition to Adult Care
Focus Groups
Social Support
Young Adult
Photography
Qualitative Research
Adult

@article {pmid40888030,
year = {2025},
author = {Yang, H and Wang, Y},
title = {From Fragmentation to Resolution: High-Fidelity Genome Assembly of Zancudomyces culisetae through Comparative Insights from PacBio, Nanopore, and Illumina Sequencing.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf204},
pmid = {40888030},
issn = {2160-1836},
abstract = {Zancudomyces culisetae is an obligate symbiotic fungus inhabiting the digestive tracts of aquatic insect larvae, including black flies, midges, and mosquitoes. With a global distribution and high prevalence in disease-transmitting insects, Z. culisetae serves as a model for studying insect gut fungi. A previous draft genome assembly using Illumina short reads provided insights into its genome composition, such as a low GC ratio and evidence of horizontal gene transfer. However, its fragmented nature has limited deeper exploration of the evolutionary mechanisms shaping these gut symbionts. To address this gap, we generated a wealth of genomic resources for Z. culisetae using multiple sequencing platforms, including Illumina, Oxford Nanopore, PacBio-CLR (Complete Long Reads), and PacBio-HiFi (High Fidelity). This also provides an opportunity to compare these popular sequencing methods to suggest the optimal approach for fungal genome assembly. Our results suggest that PacBio-HiFi produced the most complete assembly, yielding a 27.8 Mb genome size with 26 contigs, representing the highest-quality genome of insect gut fungi to date. Additionally, we generated transcriptomic data to support genome annotation, identifying 8,484 protein-coding genes. Despite the improved genome quality, Z. culisetae lacks approximately 20% of Benchmarking Universal Single-Copy Orthologue (BUSCO) commonly found in fungi, reflecting adaptations to its obligate symbiotic lifestyle. This study not only provides valuable genomic resources for insect gut fungal research but also evaluates the strengths and limitations of current genome sequencing and assembly approaches, offering best practices for fungal genome analysis and genetic research.},
}

@article {pmid40885196,
year = {2025},
author = {Li, L and Yang, Q and Liu, M and Lin, S and Hua, W and Shi, D and Yan, J and Shi, X and Hoffmann, AA and Zhu, B and Liang, P},
title = {Symbiotic bacteria mediate chemical-insecticide resistance but enhance the efficacy of a biological insecticide in diamondback moth.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.004},
pmid = {40885196},
issn = {1879-0445},
abstract = {Insecticide resistance has been a major challenge for pest management worldwide. Here, we investigated how gut symbiotic bacteria in insects might affect resistance to chemical (organophosphate) and biological (Bacillus thuringiensis) insecticides in different ways to create opportunities for strategic pesticide rotations. Using the diamondback moth (Plutella xylostella) as the target pest, we demonstrated that long-term exposure to chlorpyrifos (an organophosphate insecticide) promotes the proliferation of the gut symbiont Enterococcus mundtii in P. xylostella populations, resulting in chlorpyrifos resistance in field populations across China that correlates closely with the abundance of this bacterium. Metabolic analysis revealed that E. mundtii can directly metabolize chlorpyrifos via a conserved cytochrome P450 enzyme in the genus Enterococcus. However, the accumulation of E. mundtii in the gut of chlorpyrifos-resistant populations may increase their susceptibility to Bacillus thuringiensis toxins, resulting in the increased efficacy of Bacillus thuringiensis in populations with high chemical insecticide resistance. The gut barrier disruption caused by Bacillus thuringiensis promotes invasion of E. mundtii from the gut into the hemolymph, leading to death by septicemia to enhance susceptibility. The study highlights an interaction between resistance to chemically synthesized and biological insecticides mediated by gut symbiotic bacteria and suggests a control strategy involving chemical/biological pesticide rotations that may apply to other cases of resistance to chemically synthesized insecticides.},
}

@article {pmid40885195,
year = {2025},
author = {Grujcic, V and Mehrshad, M and Vigil-Stenman, T and Lundin, D and Foster, RA},
title = {Stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.003},
pmid = {40885195},
issn = {1879-0445},
abstract = {A few genera of diatoms that form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. are widespread in the open ocean. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, and endobiont) that is reflected in the symbiont genome size and content. In this study, we analyzed genomes derived from cultures and environmental metagenome-assembled genomes of Richelia symbionts, focusing on characters indicative of genome evolution. Our results show an enrichment of short-length transposases and pseudogenes in the periplasmic symbiont genomes, suggesting an active and transitionary period in genome evolution. By contrast, genomes of endobionts exhibited fewer transposases and pseudogenes, reflecting advanced stages of genome reduction. Pangenome analyses identified that endobionts streamline their genomes and retain most genes in the core genome, whereas periplasmic symbionts and epibionts maintain larger flexible genomes, indicating higher genomic plasticity compared with the genomes of endobionts. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by the absence of specific pathways (e.g., cytochrome bd ubiquinol oxidase and lipid A) that increase both dependency and direct interactions with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.},
}

@article {pmid40884179,
year = {2025},
author = {Liu, Y and Feng, R and Zhao, Y and Guo, X and Ding, J and Liu, S and Wang, Y and Zhu, J and Li, X},
title = {Solar-Mechano Symbiosis Dual-Mode Janus Bioaerogel for Context-Adaptive Atmospheric Water Harvesting Beyond Solar Reliance.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e12244},
doi = {10.1002/adma.202512244},
pmid = {40884179},
issn = {1521-4095},
support = {22305192//National Natural Science Foundation of China/ ; 52372225//National Natural Science Foundation of China/ ; 22261142666//National Natural Science Foundation of China/ ; 52172237//National Natural Science Foundation of China/ ; KF2301//Opening Project of Engineering Research Center of Eco-friendly Polymeric Materials, Ministry of Education/ ; //Fundamental Research Funds for the Central Universities/ ; 2024YFF0506000//the National Key Research and Development Program of China/ ; 2025JC-QYCX-037//the Shaanxi Science Foundation/ ; 20250425//the Shaanxi Association for Science and Technology Youth Talent Support Program/ ; },
abstract = {Solar-driven sorption-based atmospheric water harvesting (SS-AWH) offers promise for addressing global freshwater scarcity. However, the SS-AWH heavily relies on favorable and sustained solar irradiation; yet real-world solar irradiation exhibits significant spatiotemporal fluctuations, limiting its sustainable application, as non/low-light conditions sharply reduce water productivity. This constraint is fundamentally due to the singleness of the water release pathway via photothermal desorption. Here, a novel dual-mode bio-based Janus aerogel (DBJA) is presented, enabling efficient, all-weather, multi-scenario atmospheric water harvesting via selectively solar-driven and compression-activated water release. The Janus structure optimizes mass/heat transfer between hygroscopic and photothermal domains, achieving the most balanced adsorption-desorption kinetics and compression-recovery strength for solar-mechano symbiosis. Under favorable sunlight, DBJA demonstrates a competitive water release efficiency of 1.32 g g[-1] day[-1] outdoors. Crucially, without solar irradiation, DBJA achieves a total water productivity of 12.80 g g[-1] over 5-cycle adsorption-compression with 98% volume recovery and is stable within 50 cycles. Enhanced physical inlay and multiple chemical interactions ensure limited leakage of Li[+] ions during compression, and the collected water easily conforms to the World Health Organization (WHO) drinking water standards. This work provides a flexible approach for sustainable atmospheric water harvesting beyond solar reliance through multi-mode synergy and gradient architecture.},
}

@article {pmid40882880,
year = {2025},
author = {Niu, Z and Guo, H and Li, D and Xu, Y and Liu, J and Xiao, Y and Li, W and Promboon, A and Xia, Q and Goldsmith, MR and Mita, K},
title = {Characterizing the Symbiotic Relationship between Wolbachia (wSpic) and Spodoptera picta (Lepidoptera: Noctuidae): From Genome to Phenotype.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104396},
doi = {10.1016/j.ibmb.2025.104396},
pmid = {40882880},
issn = {1879-0240},
abstract = {Wolbachia is a genus of symbiotic bacteria prevalent in arthropods, with diverse effects on host reproduction and fecundity; however, it is unclear how Wolbachia modulates the host reproductive system. In this study, a novel Wolbachia strain, wSpic, was identified in the Noctuid moth Spodoptera picta and its effect on the reproduction of this host was investigated. We sequenced and annotated the 1,339,720 bp genome of wSpic. We identified a total of five WO phage regions in the genome and found no evidence of any plasmids associated with wSpic. Evolutionary analysis revealed that wSpic belongs to supergroup B and has undergone horizontal transmission between S. picta and Trichogramma pretiosum, a wasp parasitoid of insect eggs. The removal of Wolbachia by antibiotic treatment resulted in significantly decreased fecundity and abnormal development of S. picta ovaries, but no differences in egg hatching rate. An integrated transcriptome and proteome analysis indicated that major molecular pathways for Wolbachia-induced reproduction fitness benefits include its effects on insect juvenile hormone, vitellogenesis, choriogenesis, and nutritional metabolism. Our findings demonstrate that wSpic plays a critical role in promoting ovary development and sustaining fecundity in S. picta hosts.},
}

@article {pmid40882272,
year = {2025},
author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M},
title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127108},
doi = {10.1016/j.jenvman.2025.127108},
pmid = {40882272},
issn = {1095-8630},
abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.},
}

@article {pmid40881295,
year = {2025},
author = {Hu, X and Li, H and Liu, A and Zhang, Z},
title = {Editorial: Microbial symbiosis and infectious disease dynamics in reptiles and wildfowl.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673344},
doi = {10.3389/fmicb.2025.1673344},
pmid = {40881295},
issn = {1664-302X},
}

@article {pmid40880884,
year = {2024},
author = {Padilla-Serrato, JG and Soriano-Honorato, LD and Kuk-Dzul, JG and Flores-Garza, R and Torreblanca-Ramírez, C and Campos, E},
title = {Rediscovery of Mesotheres unguifalcula (Glassell, 1936) (Crustacea: Brachyura: Pinnotheridae) with Remarks on the Symbiotic Relationship with its New Host, the Spindle Sea Snail Leucozonia cerata (W. Wood, 1828) (Mollusa: Gastropoda: Fasciolariidae).},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e44},
doi = {10.6620/ZS.2024.63-44},
pmid = {40880884},
issn = {1810-522X},
abstract = {The symbiotic pinnotherid crab Mesotheres unguifalcula was rediscovered in Acapulco Guerrero, Mexico, and was found infesting the spindle sea snail Leucozonia cerata (Fasciolaridae), a new host record for this crab. A total of 432 snails were collected in 2020, with a prevalence of 77%, well explained by the host width frequency. Monthly prevalence varied from 54% to 90%, and the mean intensity was 1.4 +/- 0.5 crabs per host. The sex ratio of snails was 1:1, and the crab did not prefer to infest males or females. The sex ratio of the crabs was positively skewed towards females. Crabs infested both small and large snails; however, most infested snails ranged between 20 and 40 mm in width. Prevalence increased with the host size: with hosts smaller than 30 mm experiencing an average of 53% infestation, while those from 30 mm to 52 mm averaged 93% infestation. The number of crabs by host varied from 1 to 3; solitary females and males were dominant (51%), followed by heterosexual couples (24%) and other combinations that included homosexual couples and triads, which barely represented 2%. Although there are many heterosexual couples, monogamy is ruled out due to the higher number of solitary males and females and the lower number of heterosexual couples compared to those statistically expected. The available evidence about the life history of Mesotheres unguialcula, like that of other studied species of the subfamily Pinnotherinae sensu stricto, suggests a pure-search polygynandry of sedentary females as its mating system (i.e., larger, solitary, and sedentary females, and smaller males who, in reproductive season, are roaming from one host to another in search of females receptive to copulation).},
}

@article {pmid40877949,
year = {2025},
author = {Gonçalves, CS and Catta-Preta, CMC and Repolês, BM and Ferreira, WRR and Morini, FS and Mottram, JC and Cavalcanti, DP and de Souza, W and Fragoso, SP and Machado, CR and Motta, MCM},
title = {From mitochondrial DNA arrangement to repair: a kinetoplast-associated protein with different roles in two trypanosomatid species.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {366},
pmid = {40877949},
issn = {1756-3305},
support = {APQ-02533-24, BPD-00548-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 305299/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; E-26/201.011/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*DNA, Kinetoplast/genetics/metabolism ; *Trypanosoma cruzi/genetics/radiation effects/metabolism ; *DNA, Mitochondrial/genetics ; *Trypanosomatina/genetics/metabolism ; *Protozoan Proteins/genetics/metabolism ; DNA Replication ; *DNA Repair ; DNA, Protozoan/genetics ; Mitochondria/genetics ; Animals ; },
abstract = {BACKGROUND: One of the most intriguing and unusual features of trypanosomatids is their mitochondrial DNA, known as kinetoplast DNA (kDNA), which is organized into a network of concatenated circles. The kDNA is contained within the mitochondrial matrix and can exhibit distinct arrangements across different species and during cell differentiation. In addition to kDNA, the kinetoplast contains multiple proteins, including those involved in mitochondrial DNA topology and metabolism, such as the kinetoplast-associated proteins (KAPs). In this work, we obtained mutant cells to investigates the role of KAP7 in two trypanosomatid species, Trypanosoma cruzi and Angomonas deanei, which have distinct kinetoplast shapes and kDNA arrangements.

METHODS: For this purpose, the kDNA replication process and cell morphology and ultrastructure were evaluated using microscopy methods. Furthermore, the proliferation of cells treated with genotoxic agents, such as cisplatin and ultraviolet radiation, was analyzed.

RESULTS: In A. deanei, which contains a symbiotic bacterium, KAP7 seems to be essential, since the deletion of one KAP7 allele generated mutants with a decay in cell proliferation, as well as changes in kDNA structure and replication. In T. cruzi, null mutants exhibited disturbances in kDNA replication, although the overall topology remained unaltered. The use of cisplatin and ultraviolet (UV) radiation affected the ultrastructure of A. deanei and T. cruzi. Cisplatin promoted increased kDNA compaction in both KAP7 mutants, but only in T. cruzi did the proliferative capacity fail to recover after treatment, as was also observed following UV radiation exposure.

CONCLUSIONS: Proteins associated with DNA are evolutionarily conserved and usually perform similar functions in different organisms. Our findings reveal that KAP7 is involved in kDNA replication, but its roles differ in trypanosomatid species: in A. deanei, KAP7 is associated with kDNA arrangement, while in T. cruzi, it is related to mitochondrial metabolism, such as kDNA replication and damage response.},
}

*DNA, Kinetoplast/genetics/metabolism
*Trypanosoma cruzi/genetics/radiation effects/metabolism
*DNA, Mitochondrial/genetics
*Trypanosomatina/genetics/metabolism
*Protozoan Proteins/genetics/metabolism
DNA Replication
*DNA Repair
DNA, Protozoan/genetics
Mitochondria/genetics
Animals

@article {pmid40876856,
year = {2025},
author = {Zhai, H and Liu, M and Zhang, X and Li, X and Hu, B and Li, H and Gao, S and Wei, Y and Sun, W},
title = {Science mapping of root ecology: a bibliometric review covering 2015-2024.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcaf200},
pmid = {40876856},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Root ecology has rapidly advanced as a key discipline for understanding plant adaptive strategies and ecosystem functioning. However, comprehensive assessments of its overarching framework remain limited. This study provides a global perspective by systematically analyzing research power, intellectual bases, and research frontiers in root ecology.

METHODS: We analyzed 35,371 articles from the Web of Science Core Collection using CiteSpace and VOSviewer within a customized bibliometric framework. Co-occurrence analyses based on publication volume, citation frequency, and micro-citation labels revealed the spatiotemporal distribution of research power. Intellectual bases and research frontiers were identified through document co-citation and cluster analyses.

KEY RESULTS: The results indicate a three-phase growth trajectory in root ecology research over the past decade. China (13,027 articles) and the United States (5,679 articles) dominate global academic output. Frontiers in Plant Science (2,721 articles) and Plant and Soil (1,436 articles) are the leading journals in terms of publication volume. Key articles forming the intellectual base of this field were identified and interpreted, encompassing six major aspects, including method standardization and the root economics spectrum theory. The research frontiers were clustered into five core themes - abiotic stress, microbial symbiosis, ecological remediation, functional traits and physiological mechanisms - which were further subdivided into 19 specific research directions.

CONCLUSIONS: Root ecology is evolving from a primarily theoretical discipline toward practical applications. To support sustainable agriculture, ecological restoration, and carbon neutrality, the development of global observation networks and multifactorial stress models should be further advanced.},
}

@article {pmid40875413,
year = {2025},
author = {Liu, X and Huang, H and Gu, Y and Li, J and Zhang, X and Liu, T},
title = {Low-Cost IMU-Based System for Automated Parkinson's Subtype and Stage Classification to Support Precision Rehabilitation.},
journal = {IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TNSRE.2025.3603555},
pmid = {40875413},
issn = {1558-0210},
abstract = {Parkinson's disease (PD) is one of the most common progressive neurodegenerative disorder, for which early detection and precise rehabilitation planning are essential to alleviate its impact on quality of life and reduce societal burden. Accurate, automated PD subtype classification and staging play a key role in designing effective rehabilitation strategies while minimizing reliance on intensive expert assessments. Unlike existing automated methods that typically depend on high-cost medical imaging (e.g., MRI) or extensive sensor networks, we introduce a low-cost motion measurement system employing only two inertial measurement units (IMUs) placed on the lower legs. We propose a Symbiotic Graph Attention Network (SGAT)-based algorithm that fuses node features and whole-body features for automated PD subtype and stage detection. By establishing a symbiotic mechanism between the subtype and staging tasks and using adaptive fusion weights, our method achieves outstanding performance-subtype accuracy of 0.91 and staging accuracy of 0.85-validated on data from 46 participants. Notably, the entire detection and recognition process requires merely a simple walking task and incurs minimal time cost. The system's affordability, ease of use, and scalability underscore its substantial potential for large‑scale clinical deployment.},
}

@article {pmid40874126,
year = {2025},
author = {Niu, Y and Shao, Y and Chen, L and Wang, Y and Sun, S and Zhang, X},
title = {Social and environmental determinants of disease uncertainty in obstructive sleep apnea: a dyadic qualitative study on patients and co-residents.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1582173},
pmid = {40874126},
issn = {1664-2295},
abstract = {BACKGROUND: Obstructive sleep apnea (OSA) is a prevalent sleep disorder characterized by upper airway obstruction during sleep, leading to significant health issues and reduced quality of life. Despite its increasing prevalence, particularly among middle-aged and older adults, low awareness and treatment rates contribute to a substantial burden of disease uncertainty for both patients and their co-residents. This study aims to investigate the social and environmental determinants of disease uncertainty experienced by OSA patients and their co-residents, focusing on the impact of these factors on health behaviors and access to care.

METHODS: The study employed the theoretical model of disease uncertainty as a guiding framework and utilized the KJ method for data analysis. Using purposive sampling, 13 OSA patients and their 13 co-residents were selected to form dyads. Ethical approval was obtained, and informed consent was secured from all participants prior to the study.

RESULTS: The analysis of the interview data yielded seven major themes and 19 sub-themes. (1) "The Shadow of Knowing Little"; (2) "The Fog of Night and Day"; (3) "Symbiotic Suffering"; (4) "The Hidden Costs"; (5) "Delay in Seeking Medical Care"; (6) "Complex Choices"; (7) "Vacancies Calling for Attention."

CONCLUSION: The findings underscore that OSA patients and their co-residents face considerable uncertainty related to disease awareness, symptom experiences, medical decision-making, treatment plans, and social support. This uncertainty leads to delays in seeking care and poor treatment adherence. To mitigate these issues, it is recommended to enhance public health education on OSA, improve disease awareness and self-management skills among patients and their families, and better integrate medical resources and social support networks. These interventions should address the social and environmental determinants of health to reduce the burden of disease uncertainty and improve overall health outcomes.},
}

@article {pmid40873703,
year = {2025},
author = {Racioppo, A and Martins, V and Speranza, B and Laranjo, M},
title = {Editorial: Innovative strategies for enhancing crop productivity and soil health using PGPB and nano-organics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1672604},
doi = {10.3389/fmicb.2025.1672604},
pmid = {40873703},
issn = {1664-302X},
}

@article {pmid40873650,
year = {2025},
author = {Niu, Y and Feng, J and Ma, J and Xiao, T and Yuan, W},
title = {Targeting the Tumor Microbiota in Cancer Therapy Basing on Nanomaterials.},
journal = {Exploration (Beijing, China)},
volume = {5},
number = {4},
pages = {e20210185},
pmid = {40873650},
issn = {2766-2098},
abstract = {Intra-tumoral microbiota, which is a potential component of the tumor microenvironment (TME), has been emerging as a key participant and driving factor in cancer. Previously, due to technical issues and low biological content, little was known about the microbial community within tumors. With the development of high-throughput sequencing technology and molecular biology techniques, it has been demonstrated that tumors harbor highly heterogeneous symbiotic microbial communities, which affect tumor progression mechanisms through various pathways, such as inducing DNA damage, activating carcinogenic pathways, and inducing an immunesuppressive environment. Faced with the harmful microbial communities in the TME, efforts have been made to develop new technologies specifically targeting the microbiome and tumor microecology. Given the success of nanotechnology in cancer diagnosis and treatment, the development of nanotechnology to regulate microscale and molecular-scale interactions occurring in the microbiome and tumor microecology holds promise for providing new approaches for cancer therapy. This article reviews the latest progress in this field, including the microbial community within tumors and its pro-cancer mechanisms, as well as the anti-tumor strategies targeting intra-tumoral microorganisms using nanotechnology. Additionally, this article delivers prospects for the potential clinical significance and challenges of anti-tumor strategies against intra-tumoral microorganisms.},
}

@article {pmid40872788,
year = {2025},
author = {Jeon, J and Kwon, M and Lee, BC and Kil, EJ},
title = {Comparative Endosymbiont Community Structures of Nonviruliferous and Rice Stripe Virus-Viruliferous Laodelphax striatellus (Hemiptera: Delphacidae) in Korea.},
journal = {Viruses},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/v17081074},
pmid = {40872788},
issn = {1999-4915},
support = {PJ01556601//Rural Development Administration/ ; },
mesh = {Animals ; *Hemiptera/microbiology/virology ; *Symbiosis ; *Tenuivirus/physiology ; RNA, Ribosomal, 16S/genetics ; Insect Vectors/microbiology/virology ; Republic of Korea ; Oryza/virology ; Wolbachia/genetics ; Plant Diseases/virology ; Burkholderia/genetics ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/genetics/isolation & purification ; Microbiota ; Phylogeny ; Rickettsia/genetics/isolation & purification ; },
abstract = {Insects and their bacterial endosymbionts form intricate ecological relationships, yet their role in host-pathogen interactions are not fully elucidated. The small brown planthopper (Laodelphax striatellus), a polyphagous pest of cereal crops, acts as a key vector for rice stripe virus (RSV), a significant threat to rice production. This study aimed to compare the endosymbiont community structures of nonviruliferous and RSV-viruliferous L. striatellus populations using 16S rRNA gene sequencing with high-throughput sequencing technology. Wolbachia was highly dominant in both groups; however, the prevalence of other endosymbionts, specifically Rickettsia and Burkholderia, differed markedly depending on RSV infection. Comprehensive microbial diversity and composition analyses revealed distinct community structures between nonviruliferous and RSV-viruliferous populations, highlighting potential interactions and implications for vector competence and virus transmission dynamics. These findings contribute to understanding virus-insect-endosymbiont dynamics and could inform strategies to mitigate viral spread by targeting symbiotic bacteria.},
}

Animals
*Hemiptera/microbiology/virology
*Symbiosis
*Tenuivirus/physiology
RNA, Ribosomal, 16S/genetics
Insect Vectors/microbiology/virology
Republic of Korea
Oryza/virology
Wolbachia/genetics
Plant Diseases/virology
Burkholderia/genetics
High-Throughput Nucleotide Sequencing
Bacteria/classification/genetics/isolation & purification
Microbiota
Phylogeny
Rickettsia/genetics/isolation & purification

@article {pmid40872311,
year = {2025},
author = {Etebari, K and Tugaga, AM and Divekar, G and Uelese, OA and Tusa, SSA and Vaega, E and Sasulu, H and Uini, L and Ren, Y and Furlong, MJ},
title = {Characterising the Associated Virome and Microbiota of Asian Citrus Psyllid (Diaphorina citri) in Samoa.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/pathogens14080801},
pmid = {40872311},
issn = {2076-0817},
support = {HORT/2016/185//Australian Centre for International Agricultural Research/ ; },
mesh = {Animals ; *Hemiptera/virology/microbiology ; *Virome/genetics ; *Microbiota ; Plant Diseases/microbiology ; *Citrus/microbiology/parasitology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Insect Vectors/microbiology/virology ; },
abstract = {The Asian citrus psyllid (Diaphorina citri) is an economically important pest of citrus as it is a vector of the bacterium (Candidatus Liberibacter asiaticus, CLas) that causes huanglongbing disease (HLB). Understanding the virome of D. citri is important for uncovering factors that influence vector competence, to support biosecurity surveillance, and to identify candidate agents for biological control. Previous studies have identified several D. citri-associated viruses from various geographical populations of this pest. To further investigate virus diversity in this pest, high-throughput sequencing was used to analyse D. citri populations from the Samoan islands of Upolu and Savai'i. Eleven novel viruses from the Yadokariviridae, Botourmiaviridae, Nodaviridae, Mymonaviridae, Partitiviridae, Totiviridae, and Polymycoviridae were identified as well as some that corresponded to unclassified groups. In addition, microbiome analysis revealed the presence of several endosymbiotic microorganisms, including Wolbachia, as well as some plant pathogenic fungi, including Botrytis cinerea. However, the causative agent of HLB disease (CLas) was not detected in the RNA-Seq data. These findings highlight the complex and diverse microbiota associated with D. citri and suggest potential interactions and dynamics between microorganisms and psyllid-associated viruses. Further research is needed to understand the ecological significance of these discoveries, and whether the novel viruses play a role in regulating field populations of the psyllid.},
}

Animals
*Hemiptera/virology/microbiology
*Virome/genetics
*Microbiota
Plant Diseases/microbiology
*Citrus/microbiology/parasitology
High-Throughput Nucleotide Sequencing
Phylogeny
Insect Vectors/microbiology/virology

@article {pmid40872269,
year = {2025},
author = {Britto Martins de Oliveira, J and Barbieri, M and Corrêa-Junior, D and Schmitt, M and Santos, LLR and Bahia, AC and Parente, CET and Frases, S},
title = {Urban Mangroves Under Threat: Metagenomic Analysis Reveals a Surge in Human and Plant Pathogenic Fungi.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/pathogens14080759},
pmid = {40872269},
issn = {2076-0817},
support = {CNE//FAPERJ/ ; 001//CAPES/ ; BP//CNPQ/ ; },
mesh = {*Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification ; Humans ; *Wetlands ; Ecosystem ; Biodiversity ; Mycobiome ; Geologic Sediments/microbiology ; },
abstract = {Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness-28% lower than expected for similar ecosystems-likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments.},
}

*Metagenomics/methods
*Fungi/genetics/classification/isolation & purification
Humans
*Wetlands
Ecosystem
Biodiversity
Mycobiome
Geologic Sediments/microbiology

@article {pmid40872079,
year = {2025},
author = {Xia, M and Tang, L and Zhai, H and Liu, Y and Zhang, L and Chen, D},
title = {Genome-Wide Identification and Evolutionary Analysis of the GATA Transcription Factor Family in Nitrogen-Fixing Legumes.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {16},
pages = {},
doi = {10.3390/plants14162456},
pmid = {40872079},
issn = {2223-7747},
support = {32400295//National Natural Science Foundation of China/ ; 0205-6602-A12201//Research Startup Funding from Hainan Institute of Zhejiang University/ ; },
abstract = {GATA transcription factors are crucial for plant development and environmental responses, yet their roles in plant evolution and root nodule symbiosis are still not well understood. This study identified GATA genes across the genomes of 77 representative plant species, revealing that this gene family originated in Charophyta and significantly expanded in both gymnosperms and angiosperms. Phylogenetic analyses, along with examinations of conserved motifs and cis-regulatory elements in Glycine max and Arabidopsis, clearly demonstrated structural and functional divergence within the GATA family. Chromosomal mapping and synteny analysis indicated that GATA gene expansion in soybean primarily resulted from whole-genome duplication events. These genes also exhibit high conservation and signs of purifying selection in Glycine max, Lotus japonicus, and Medicago truncatula. Furthermore, by integrating phylogenetic and transcriptomic data from eight nitrogen-fixing legume species, several GATA genes were identified as strongly co-expressed with NIN1, suggesting their potential co-regulatory roles in nodule development and symbiosis. Collectively, this study offers a comprehensive overview of the evolutionary dynamics of the GATA gene family and highlights their potential involvement in root nodule symbiosis in legumes, thus providing a theoretical foundation for future mechanistic studies.},
}

@article {pmid40871461,
year = {2025},
author = {Yang, T and Qi, Z and Wang, H and Zheng, P and Kao, SJ and Diao, X},
title = {Seasonal Variation in In Hospite but Not Free-Living, Symbiodiniaceae Communities Around Hainan Island, China.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081958},
pmid = {40871461},
issn = {2076-2607},
support = {2021M702729//China Postdoctoral Science Foundation/ ; 41967032//National Natural Science Foundation of China/ ; },
abstract = {Coral reefs are increasingly threatened by global climate change, and mass bleaching and mortality events caused by elevated seawater temperature have led to coral loss worldwide. Hainan Island hosts extensive coral reef ecosystems in China, yet seasonal variation in Symbiodiniaceae communities within this region remains insufficiently understood. We aimed to investigate the temperature-driven adaptability regulation of the symbiotic Symbiodiniaceae community in reef-building corals, focusing on the environmental adaptive changes in its community structure in coral reefs between cold (23.6-24.6 °C) and warm (28.2-30.6 °C) months. Symbiodiniaceae shuffling and rare genotype turnover were discovered in adaptability variations in the symbiotic Symbiodiniaceae community between two months. Symbiodiniaceae genetic diversity increased during warm months, primarily due to temporal turnover of rare genotypes within the Cladocopium and Durusdinium genera. Coral Favites, Galaxea, and Porites exhibited the shuffling of Symbiodiniaceae between tolerant Durusdinium and sensitive Cladocopium. Symbiodiniaceae interactions in G. fascicularis and P. lutea exhibited the highest levels of stability with the increase in temperature, whereas the interactions in A. digitifera and P. damicornis showed the lowest levels of stability. Rare genotypes functioned as central hubs and important roles within Symbiodiniaceae communities, exhibiting minimal responsiveness to temperature fluctuations while maintaining community structural stability. The temperature-driven adaptability regulation of symbiotic Symbiodiniaceae could be achieved by Symbiodiniaceae shuffling and rare genotype turnover. The process might be aggravated by concurrent adverse factors, including elevated salinity, pollution, and anthropogenic disturbance. These findings provide insights into how the Symbiodiniaceae community influences the adaptation and resilience of coral hosts to temperature fluctuations in coral reefs. Furthermore, they may contribute to assessing the reef-building coral's capacity to withstand environmental stressors associated with global climate change.},
}

@article {pmid40871434,
year = {2025},
author = {Rincón-Rosales, R and Díaz-Hernández, M and Manzano-Gómez, LA and Rincón-Molina, FA and Ruíz-Valdiviezo, VM and Gen-Jiménez, A and Villalobos-Maldonado, JJ and Maldonado-Gómez, JC and Rincón-Molina, CI},
title = {Analysis of the Bacterial Community and Fatty Acid Composition in the Bacteriome of the Lac Insect Llaveia axin axin.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081930},
pmid = {40871434},
issn = {2076-2607},
support = {22004.25-P//Tecnológico Nacional de México/ ; 21914.25-P//Tecnológico Nacional de México/ ; },
abstract = {Microbial symbioses play crucial roles in insect physiology, contributing to nutrition, detoxification, and metabolic adaptations. However, the microbial communities associated with the lac insect Llaveia axin axin, an economically significant species used in traditional lacquer production, remain poorly characterized. In this study, the bacterial diversity and community structure of L. axin axin were investigated using both culture-dependent and culture-independent (metagenomic) approaches, combined with fatty acid profile analysis. The insects were bred at the laboratory level, in controlled conditions, encompassing stages from eggs to adult females. Bacterial strains were isolated from bacteriomes and identified through 16S rRNA gene amplification and genomic fingerprinting through ARDRA analysis. Metagenomic DNA was sequenced using the Illumina MiSeq platform, and fatty acid profiles were determined by gas chromatography-mass spectrometry (GC-MS). A total of 20 bacterial strains were isolated, with Acinetobacter, Moraxella, Pseudomonas, and Staphylococcus detected in first-instar nymphs; Methylobacterium, Microbacterium, and Bacillus in pre-adult females; and Bacillus and Microbacterium in adults. Metagenomic analysis revealed key genera including Sodalis, Blattabacterium, and Candidatus Walczuchella, with Sodalis being predominant in early stages and Blattabacteriaceae in adults. Fatty acid analysis identified palmitic, oleic, linoleic, arachidic, and stearic acids, with stearic acid being the most abundant. These results suggest that dominant bacteria contribute to lipid biosynthesis and metabolic development in L. axin axin.},
}

@article {pmid40871425,
year = {2025},
author = {Danilova, OV and Salova, VD and Oshkin, IY and Naumoff, DG and Ivanova, AA and Suzina, NE and Dedysh, SN},
title = {Isolation of Ultra-Small Opitutaceae-Affiliated Verrucomicrobia from a Methane-Fed Bioreactor.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081922},
pmid = {40871425},
issn = {2076-2607},
support = {25-24-00426//Russian Science Foundation (RSF)/ ; },
abstract = {The bacterial phylum Verrucomicrobiota accommodates free-living and symbiotic microorganisms, which inhabit a wide range of environments and specialize in polysaccharide degradation. Due to difficulties in cultivation, much of the currently available knowledge about these bacteria originated from cultivation-independent studies. A phylogenetic clade defined by the free-living bacterium from oilsands tailings pond, Oleiharenicola alkalitolerans, and the symbiont of the tunicate Lissoclinum sp., Candidatus Didemniditutus mandelae, is a poorly studied verrucomicrobial group. This clade includes two dozen methagenome-assembled genomes (MAGs) retrieved from aquatic and soil habitats all over the world. A new member of this clade, strain Vm1, was isolated from a methane-fed laboratory bioreactor with a Methylococcus-dominated methane-oxidizing consortium and characterized in this study. Strain Vm1 was represented by ultra-small, motile cocci with a mean diameter of 0.4 µm that grew in oxic and micro-oxic conditions at temperatures between 20 and 42 °C. Stable development of strain Vm1 in a co-culture with Methylococcus was due to the ability to utilize organic acids excreted by the methanotroph and its exopolysaccharides. The finished genome of strain Vm1 was 4.8 Mb in size and contained about 4200 predicted protein-coding sequences, including a wide repertoire of CAZyme-encoding genes. Among these CAZymes, two proteins presumably responsible for xylan and arabinan degradation, were encoded in several MAGs of Vm1-related free-living verrucomicrobia, thus offering an insight into the reasons behind wide distribution of these bacteria in the environment. Apparently, many representatives of the Oleiharenicola-Candidatus Didemniditutus clade may occur in nature in trophic associations with methanotrophic bacteria, thus participating in the cycling of methane-derived carbon.},
}

@article {pmid40871343,
year = {2025},
author = {Chen, X and Lu, Y and Liu, X and Gu, Y and Li, F},
title = {Trichoderma: Dual Roles in Biocontrol and Plant Growth Promotion.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081840},
pmid = {40871343},
issn = {2076-2607},
support = {Qiankehejichu-ZK [2022] Zhongdian 033//Natural Science Foundation of Guizhou Province/ ; },
abstract = {The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma's biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various enzymes, secondary metabolites, and volatile organic compounds, Trichoderma effectively suppresses plant pathogens, promotes root development, and primes plant immune responses. This review details the evolutionary adaptations of Trichoderma, which has transitioned from saprotrophism to mycoparasitism and established beneficial symbiotic relationships with plants. It also highlights the ecological versatility of Trichoderma in colonizing plant roots and improving soil health, while emphasizing its role in mitigating both biotic and abiotic stressors. With increasing recognition as a biostimulant and biocontrol agent, Trichoderma has become a key player in reducing chemical inputs and advancing eco-friendly farming practices. This review addresses challenges such as strain selection, formulation stability, and regulatory hurdles and concludes by advocating for continued research to optimize Trichoderma's applications in addressing climate change, enhancing food security, and promoting a sustainable agricultural future.},
}

@article {pmid40871230,
year = {2025},
author = {Iram, N and Ren, Y and Zhao, R and Zhao, S and Dong, C and Han, Y and Zhang, Y},
title = {Deciphering Soil Keystone Microbial Taxa: Structural Diversity and Co-Occurrence Patterns from Peri-Urban to Urban Landscapes.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081726},
pmid = {40871230},
issn = {2076-2607},
support = {[No.32060011, 32160007, 32260003]//The National Natural Science Foundation of China/ ; [Qian Ke He [2020] 6005]//"Hundred" Talent Projects of Guizhou Province/ ; [GNYL [2017]009]//Construction Program of Biology First-class Discipline in Guizhou/ ; },
abstract = {Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (p < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (p < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure.},
}

@article {pmid40870637,
year = {2025},
author = {Qi, Q and Li, B and Zhang, X and Chen, X and Chen, H and King-Jones, K},
title = {Ecological Significance of a Novel Nitrogen Fixation Mechanism in the Wax Scale Insect Ericerus pela.},
journal = {Insects},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/insects16080836},
pmid = {40870637},
issn = {2075-4450},
support = {CAFYBB2019SZ005//Central Non-profit Research Institution of CAF/ ; },
abstract = {As a sessile wax scale insect, Ericerus pela heavily relies on its host plant for nutrition. While E. pela utilizes the nitrogen-poor plant sap as its primary nutrient source, the mechanisms by which this insect overcomes the nitrogen deficiency are poorly understood. In this study, we first confirm the nitrogen fixation capability of E. pela through isotopic tracer experiments and the acetylene reduction assay, which demonstrate that female adults exhibit an efficient nitrogen fixation rate. High-throughput sequencing further revealed 42 nitrogen-fixing bacterial species in the tissues of E. pela, most notably including Rhizobiales and Methylobacterium as the dominant species converting atmospheric nitrogen to ammonia. Several critical genes involved in nitrogen fixation, ammonia transporting, amino acid synthesis, and transportation were determined to be transcriptionally active across different developmental stages of E. pela. In addition, the symbiotic fungus Ophiocordyceps-located in the fat body of E. pela-was found to be capable of synthesizing all amino acids, including the essential amino acids required for the survival of E. pela. Taken together, this study demonstrates that E. pela has evolved a highly effective nitrogen acquisition system driven by symbiotic microorganisms, ensuring a sufficient nitrogen supply and enabling it to thrive on nitrogen-deficient food sources. Our findings reveal a unique evolutionary adaptation in which E. pela leveraged both bacterial nitrogen fixation and fungal amino acid synthesis to bolster its growth and development.},
}

@article {pmid40870591,
year = {2025},
author = {Siden-Kiamos, I and Pantidi, G and Vontas, J},
title = {The Journey of the Bacterial Symbiont Through the Olive Fruit Fly: Lessons Learned and Open Questions.},
journal = {Insects},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/insects16080789},
pmid = {40870591},
issn = {2075-4450},
abstract = {Dysbiosis is a strategy to control insect pests through disrupting symbiotic bacteria essential for their life cycle. The olive fly, Bactrocera oleae, has been considered a suitable system for dysbiosis, as the insect is strictly dependent on its unique symbiont Candidatus Erwinia dacicola. Here, we review older and recent results from studies of the interaction of the symbiont and its host fly. We then discuss possible methods for disrupting the symbiosis as a means to control the fly. Specifically, we summarize studies using microscopy methods that have investigated in great detail the organs where the bacterium resides and it is always extracellular. Furthermore, we discuss how genome sequences of both host and bacterium can provide valuable resources for understanding the interaction and transcriptomic analyses that have revealed important insights that can be exploited for dysbiosis strategies. We also assess experiments where compounds have been tested against the symbiont. The hitherto limited efficacy in decreasing bacterial abundance suggests that novel molecules and/or new ways for the delivery of agents will be important for successful dysbiosis strategies. Finally, we discuss how gene drive methods could be implemented in olive fly control, though a number of hurdles would need to be overcome.},
}

@article {pmid40869242,
year = {2025},
author = {Khatoon, A and Aslam, MM and Komatsu, S},
title = {Role of Plant-Derived Smoke Solution on Plants Under Stress.},
journal = {International journal of molecular sciences},
volume = {26},
number = {16},
pages = {},
doi = {10.3390/ijms26167911},
pmid = {40869242},
issn = {1422-0067},
support = {This research was funded by the University-Special Research Grants (Practical application, 2025)//Fukui University of Technology/ ; },
mesh = {*Stress, Physiological/drug effects ; *Smoke ; *Plants/metabolism ; Reactive Oxygen Species/metabolism ; Antioxidants/metabolism ; Plant Development/drug effects ; },
abstract = {Plants are constantly exposed to various environmental challenges, such as drought, flooding, heavy metal toxicity, and pathogen attacks. To cope with these stresses, they employ several adaptive strategies. This review highlights the potential of plant-derived smoke (PDS) solution as a natural biostimulant for improving plant health and resilience, contributing to both crop productivity and ecological restoration under abiotic and biotic stress conditions. Mitigating effects of PDS solution against various stresses were observed at morphological, physiological, and molecular levels in plants. PDS solution application involves strengthening the cell membrane by minimizing electrolyte leakage, which enhances cell membrane stability and stomatal conductance. The increased reactive-oxygen species were managed by the activation of the antioxidant system including ascorbate peroxidase, superoxide dismutase, and catalase to meet oxidative damage caused by challenging conditions imposed by flooding, drought, and heavy metal stress. PDS solution along with other by-products of fire, such as charred organic matter and ash, can enrich the soil by slightly increasing its pH and improving nutrient availability. Additionally, some studies indicated that PDS solution may influence phytohormonal pathways, particularly auxins and gibberellic acids, which can contribute to root development and enhance symbiotic interactions with soil microbes, including mycorrhizal fungi. These combined effects may support overall plant growth, though the extent of PDS contribution may vary depending on species and environmental conditions. This boost in plant growth contributes to protecting the plants against pathogens, which shows the role of PDS in enduring biotic stress. Collectively, PDS solution mitigates stress tolerance in plants via multifaceted changes, including the regulation of physico-chemical responses, enhancement of the antioxidant system, modulation of heavy metal speciation, and key adjustments of photosynthesis, respiration, cell membrane transport, and the antioxidant system at genomic/proteomic levels. This review focuses on the role of PDS solution in fortifying plants against environmental stresses. It is suggested that PDS solution, which already has been determined to be a biostimulant, has potential for the revival of plant growth and soil ecosystem under abiotic and biotic stresses.},
}

*Stress, Physiological/drug effects
*Smoke
*Plants/metabolism
Reactive Oxygen Species/metabolism
Antioxidants/metabolism
Plant Development/drug effects

@article {pmid40869153,
year = {2025},
author = {Kwon, EH and Ahmad, S and Lee, IJ},
title = {Melatonin-Producing Bacillus aerius EH2-5 Enhances Glycine max Plants Salinity Tolerance Through Physiological, Biochemical, and Molecular Modulation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {16},
pages = {},
doi = {10.3390/ijms26167834},
pmid = {40869153},
issn = {1422-0067},
mesh = {*Melatonin/biosynthesis/metabolism ; *Bacillus/metabolism/genetics ; *Salt Tolerance ; *Glycine max/microbiology/physiology/growth & development/genetics/metabolism ; Salinity ; Salt Stress ; Gene Expression Regulation, Plant ; Oxidative Stress ; Antioxidants/metabolism ; },
abstract = {Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, the global population is projected to exceed 9 billion by 2050, demanding a 70% increase in food production (UN, 2019; FAO). Agriculture, responsible for 34% of global greenhouse gas emissions, urgently needs sustainable solutions. Microbial inoculants, known as "plant probiotics," offer a promising eco-friendly alternative by enhancing crop resilience and reducing environmental impact. In this study, we evaluated the plant growth-promoting (PGP) traits and melatonin-producing capacity of Bacillus aerius EH2-5. To assess its efficacy under salt stress, soybean seedlings at the VC stage were inoculated with EH2-5 and subsequently subjected to salinity stress using 150 mM and 100 mM NaCl treatments. Plant growth parameters, the expression levels of salinity-related genes, and the activities of antioxidant enzymes were measured to determine the microbe's role in promoting plant growth and mitigating salt-induced oxidative stress. Here, our study shows that the melatonin-synthesizing Bacillus aerius EH2-5 (7.48 ng/mL at 24 h after inoculation in Trp spiked LB media) significantly improved host plant (Glycine max L.) growth, biomass, and photosynthesis and reduced oxidative stress during salinity stress conditions than the non-inculcated control. Whole genome sequencing of Bacillus aerius EH2-5 identified key plant growth-promoting and salinity stress-related genes, including znuA, znuB, znuC, and zur (zinc uptake); ptsN, aspA, and nrgB (nitrogen metabolism); and phoH and pstS (phosphate transport). Genes involved in tryptophan biosynthesis and transport, such as trpA, trpB, trpP, and tspO, along with siderophore-related genes yusV, yfhA, and yfiY, were also detected. The presence of multiple stress-responsive genes, including dnaK, dps, treA, cspB, srkA, and copZ, suggests EH2-5's genomic potential to enhance plant tolerance to salinity and other abiotic stresses. Inoculation with Bacillus aerius EH2-5 significantly enhanced soybean growth and reduced salt-induced damage, as evidenced by increased shoot biomass (29%, 41%), leaf numbers (12% and 13%), and chlorophyll content (40%, 21%) under 100 mM and 150 mM NaCl compared to non-inoculated plants. These results indicate EH2-5's strong potential as a plant growth-promoting and salinity stress-alleviating rhizobacterium. The EH2-5 symbiosis significantly enhanced a key ABA biosynthesis enzyme-related gene NCED3, dehydration responsive transcription factors DREB2A and NAC29 salinity stresses (100 mM and 150 mM). Moreover, the reduced expression of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) by 16%, 29%, and 24%, respectively, and decreased levels of malondialdehyde (MDA) and hydroxy peroxidase (H2O2) by 12% and 23% were observed under 100 mM NaCl compared to non-inoculated plants. This study demonstrated that Bacillus aerius EH2-5, a melatonin-producing strain, not only functions effectively as a biofertilizer but also alleviates plant stress in a manner comparable to the application of exogenous melatonin. These findings highlight the potential of utilizing melatonin-producing microbes as a viable alternative to chemical treatments. Therefore, further research should focus on enhancing the melatonin biosynthetic capacity of EH2-5, improving its colonization efficiency in plants, and developing synergistic microbial consortia (SynComs) with melatonin-producing capabilities. Such efforts will contribute to the development and field application of EH2-5 as a promising plant biostimulant for sustainable agriculture.},
}

*Melatonin/biosynthesis/metabolism
*Bacillus/metabolism/genetics
*Salt Tolerance
*Glycine max/microbiology/physiology/growth & development/genetics/metabolism
Salinity
Salt Stress
Gene Expression Regulation, Plant
Oxidative Stress
Antioxidants/metabolism