@article {pmid40162703,
year = {2025},
author = {Souza Beraldo, C},
title = {An interactive art activity to promote student reflection and learning about host-microbe interactions.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0006325},
doi = {10.1128/jmbe.00063-25},
pmid = {40162703},
issn = {1935-7877},
abstract = {The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects-the microbes-are invisible to human eyes. To explore how different factors shape host-microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students' conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint-representing hosts, microbes, and environmental factors, respectively-to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies' meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.},
}

@article {pmid40161817,
year = {2025},
author = {Band, VI and Gribonika, I and Stacy, A and Bouladoux, N and Mistry, S and Burns, A and Perez-Chaparro, PJ and Chau, J and Enamorado, M and Nagai, M and Bhushan, V and Golec, DP and Schwartzberg, PL and Hourigan, SK and Nita-Lazar, A and Belkaid, Y},
title = {Sulfide is a keystone metabolite for gut homeostasis and immunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641928},
pmid = {40161817},
issn = {2692-8205},
abstract = {Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.},
}

@article {pmid40160925,
year = {2025},
author = {Amirmijani, A and Pordel, A and Dehghani, K and Pourmoghaddam, MJ and Masigol, H and Grossart, HP},
title = {Two new pestalotioid fungi from tropical fruits in Iran.},
journal = {MycoKeys},
volume = {115},
number = {},
pages = {221-240},
doi = {10.3897/mycokeys.115.136469},
pmid = {40160925},
issn = {1314-4049},
abstract = {In a survey of tropical plant diseases in southern and southeastern Iran, samples of diseased Mangiferaindica and Psidiumguava leaves with necrotic symptoms were collected between 2021 and 2022. Six representative isolates of Neopestalotiopsis and Robillarda (three isolates for each) were studied using morphological characteristics as well as multi-locus phylogenetic analysis based on (i) the internal transcribed spacer (ITS) region of the nuclear rDNA, (ii) part of the translation elongation factor 1-alpha (tef1), and (iii) the β-tubulin (tub2). After morphological investigation, our phylogenetic analysis revealed that the Neopestalotiopsis and Robillarda isolates under study differed from all previously described species within these genera. Based on our polyphasic approach, two new species, including Neopestalotiopsisguava sp. nov. from necrotic Mangiferaindica and Robillardakhodaparastii sp. nov. from Psidiumguava are described and illustrated from Iran.},
}

@article {pmid40157674,
year = {2025},
author = {Wu, X and Yu, D and Ma, Y and Fang, X and Sun, P},
title = {Function and therapeutic potential of Amuc_1100, an outer membrane protein of Akkermansia muciniphila: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {142442},
doi = {10.1016/j.ijbiomac.2025.142442},
pmid = {40157674},
issn = {1879-0003},
abstract = {The gut microbiota-derived protein Amuc_1100, a key outer membrane component of Akkermansia muciniphila, has emerged as a groundbreaking therapeutic agent with unique structural and functional properties. Amuc_1100 exerts multifaceted immune-metabolic effects through novel mechanisms, including modulation of TLR2/4 and JAK/STAT pathways. This review highlights its unique multi-component structure that enables synergistic biological activity, and its pharmacological properties, which underlies its ability to enhance intestinal barrier integrity, restore microbiota balance, and suppress systemic inflammation. Crucially, Amuc_1100 demonstrates unprecedented therapeutic versatility across both intestinal disorders (e.g., inflammatory bowel disease, antibiotic-associated diarrhea) and extraintestinal conditions-notably improving neuropsychiatric symptoms via gut-serotonin axis regulation, combating cancer through CD8+ T cell activation, and mitigating cardiotoxicity via gut-heart immune crosstalk. Emerging innovations in targeted delivery systems, including gut-retentive nano-formulations and engineered probiotic vectors, further amplify its clinical potential. We critically evaluate recent advances distinguishing Amuc_1100's mechanisms from live bacterial interventions. By synthesizing evidence from preclinical models, this work positions Amuc_1100 as a prototype for next-generation microbiome-derived therapeutics, bridging microbial ecology with precision medicine.},
}

@article {pmid40152585,
year = {2025},
author = {Wang, F and Luo, J and Zhang, Z and Liu, Y and Sheng, Dh and Zhuo, L and Li, Y-z},
title = {Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives.},
journal = {mBio},
volume = {},
number = {},
pages = {e0390224},
doi = {10.1128/mbio.03902-24},
pmid = {40152585},
issn = {2150-7511},
abstract = {Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.},
}

@article {pmid40151948,
year = {2025},
author = {Šulčius, S and Alzbutas, G and Lukashevich, V},
title = {Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70042},
doi = {10.1111/1462-2920.70042},
pmid = {40151948},
issn = {1462-2920},
support = {S-LL-21-10//Lietuvos Mokslo Taryba/ ; },
mesh = {*Microbiota ; *Bacteriophages/genetics/physiology ; *Nodularia/metabolism/virology ; Bacteriolysis ; Viral Load ; Cyanobacteria/virology/metabolism/genetics ; },
abstract = {Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.},
}

*Microbiota
*Bacteriophages/genetics/physiology
*Nodularia/metabolism/virology
Bacteriolysis
Viral Load
Cyanobacteria/virology/metabolism/genetics

@article {pmid40149089,
year = {2025},
author = {Nussbaumer-Pröll, A and Hausmann, B and Weber, M and Pjevac, P and Berry, D and Zeitlinger, M},
title = {A Pilot Study on the Impact of Cranberry and Ascorbic Acid Supplementation on the Urinary Microbiome of Healthy Women: A Randomized Controlled Trial.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antibiotics14030278},
pmid = {40149089},
issn = {2079-6382},
abstract = {Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18-40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states.},
}

@article {pmid40149015,
year = {2025},
author = {Fournier, P and Pellan, L and Jaswa, A and Cambon, MC and Chataigner, A and Bonnard, O and Raynal, M and Debord, C and Poeydebat, C and Labarthe, S and Delmotte, F and This, P and Vacher, C},
title = {Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {37},
pmid = {40149015},
issn = {2524-6372},
support = {20-PCPA-0010//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.

RESULTS: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease.

CONCLUSION: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.},
}

@article {pmid40148178,
year = {2025},
author = {Hodžić, A and Duscher, GG and Alić, A and Beck, R and Berry, D},
title = {Peritrophic matrix: an important determinant of vector competence in hematophagous arthropods.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.03.005},
pmid = {40148178},
issn = {1471-5007},
abstract = {The peritrophic matrix (PM) is a non-cellular, glycan-rich structure that lines the gut epithelium of most invertebrates, including arthropod vectors that transmit diseases of public health and veterinary concern. This semipermeable barrier, functionally analogous to the vertebrate mucosal layer, separates the gut lumen from epithelial cells and provides protection against invading pathogens and their toxins. Beyond its mechanical protective role in the gut, the PM plays a crucial part in arthropod innate immunity. Here, we summarize the most recent advances in understanding the molecular mechanisms of vector-pathogen interactions in blood-feeding arthropods and discuss the significance of the PM in modulating vector competence. This knowledge could contribute to the development of novel strategies to control vector-borne infections.},
}

@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}

@article {pmid40146382,
year = {2025},
author = {Nain, D and Rana, A and Raychoudhury, R and Sen, R},
title = {Parasite-Induced Replacement of Host Microbiota: Impact of Xenos gadagkari Parasitization on the Microbiota of Polistes wattii.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {20},
pmid = {40146382},
issn = {1432-184X},
support = {DST/INSPIRE/03/2021/000175, IF200146//Department of Science and Technology, Ministry of Science and Technology, India/ ; 1061830779//Council of Scientific and Industrial Research, India/ ; CRG-2021/007010//Science and Engineering Research Board/ ; CRG-2021/007010//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Wasps/microbiology/physiology ; *Microbiota ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Host-Parasite Interactions ; Seasons ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {The study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behavior. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet a comprehensive study on the microbiota of any species of Polistes or any primitively eusocial wasp is missing. Polistes wattii is an Asian wasp, which hibernates in winter and exhibits a biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite/parasitoid Xenos gadagkari, which changes the morpho-physiology and behavior of their hosts. In this study, we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community of P. wattii and investigate the effects of seasonality, sex, and Xenos parasitism. We show that the microbiota differs in females from solitary foundress spring nests and multiple foundress summer nests. The microbiota also differs in males and females. Finally, we show that X. gadagkari parasitism replaces and homogenizes the microbiota of P. wattii. Unlike the unparasitized wasps, the microbiota of X. gadagkari parasitoids and parasitized wasps are dominated by Wolbachia and Providencia. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show that the microbiota of parasitized P. wattii becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts than previously thought.},
}

Animals
*Wasps/microbiology/physiology
*Microbiota
Female
Male
*RNA, Ribosomal, 16S/genetics
Host-Parasite Interactions
Seasons
Bacteria/genetics/classification/isolation & purification

@article {pmid40146077,
year = {2025},
author = {Savchenko, V and Yu, XA and Polz, MF and Böttcher, T},
title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1H)-quinolone Producers.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00046},
pmid = {40146077},
issn = {1554-8937},
abstract = {2-Alkyl-4(1H)-quinolones play a key role in bacterial communication, regulating biofilm formation, and virulence. Their antimicrobial properties also support bacterial survival and interspecies competition in microbial communities. In addition to the human pathogen Pseudomonas aeruginosa various species of Burkholderia and Pseudoalteromonas are known to produce 2-alkyl-4(1H)-quinolones. However, the evolutionary relationships of their biosynthetic gene clusters remain largely unexplored. To address this, we investigated the phylogeny of 2-alkyl-4(1H)-quinolone biosynthetic gene clusters, leading to the discovery of Chitinivorax as a fourth genus capable of producing 2-alkyl-4(1H)-quinolones, expanding our knowledge of the diversity of bacteria involved in quinolone-biosynthesis.},
}

@article {pmid40143451,
year = {2025},
author = {Jenkins, G and Boyd, ES and Danchin, A and Hervé, V},
title = {Microbiome Notes-Building a Library of Descriptive Microbial Ecology.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70085},
doi = {10.1111/1758-2229.70085},
pmid = {40143451},
issn = {1758-2229},
}

@article {pmid40142506,
year = {2025},
author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M},
title = {Effects of NatureKnit™, a Blend of Fruit and Vegetable Fibers Rich in Naturally Occurring Bound Polyphenols, on the Metabolic Activity and Community Composition of the Human Gut Microbiome Using the M-SHIME[®] Gastrointestinal Model.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030613},
pmid = {40142506},
issn = {2076-2607},
support = {Not applicable//VDF FutureCeuticals, Inc./ ; },
abstract = {This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit[TM]), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME[®] gastrointestinal model. A short-term single-stage colonic M-SHIME[®] experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers.},
}

@article {pmid40142410,
year = {2025},
author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL},
title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030518},
pmid = {40142410},
issn = {2076-2607},
support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; },
abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).},
}

@article {pmid40141768,
year = {2025},
author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM},
title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/life15030423},
pmid = {40141768},
issn = {2075-1729},
support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; },
abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.},
}

@article {pmid40138093,
year = {2025},
author = {Demeulenaere, É},
title = {In search of the microbial path to Terroir: a place-based history of the ecologization of French cheese microbiology, 1990-2000s.},
journal = {History and philosophy of the life sciences},
volume = {47},
number = {2},
pages = {22},
pmid = {40138093},
issn = {1742-6316},
support = {EXORIGINS//Emergence(s) Ville de Paris/ ; },
mesh = {*Cheese/microbiology/history ; France ; History, 20th Century ; *Food Microbiology/history ; Milk/history/microbiology ; Animals ; },
abstract = {At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get "cleaner" milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor "natural seeding" and enrich milk native microflora. A new approach emerged, namely "practice-driven microbial ecology" (écologie microbienne dirigée), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the "microbial (ecology) turn" described by other authors, highlighting the ecological approach developed in the 1990s-2000s by French microbiologists in search of "the microbial path to terroir".},
}

*Cheese/microbiology/history
France
History, 20th Century
*Food Microbiology/history
Milk/history/microbiology
Animals

@article {pmid40137691,
year = {2025},
author = {Maitre, A and Mateos-Hernandez, L and Kratou, M and Egri, N and Maye, J and Juan, M and Hodžić, A and Obregón, D and Abuin-Denis, L and Piloto-Sardinas, E and Fogaça, AC and Cabezas-Cruz, A},
title = {Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030206},
pmid = {40137691},
issn = {2076-0817},
mesh = {Animals ; *Ixodes/microbiology/immunology ; Mice ; *Microbiota/immunology/drug effects ; *Bacterial Vaccines/immunology/pharmacology ; Staphylococcus epidermidis/immunology/drug effects ; Rickettsia/immunology ; Tick-Borne Diseases/prevention & control/immunology/microbiology ; Female ; Vaccines, Subunit/immunology/administration & dosage ; Borrelia burgdorferi Group/immunology ; Vaccination ; Vaccines, Attenuated/immunology/administration & dosage ; },
abstract = {This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.},
}

Animals
*Ixodes/microbiology/immunology
Mice
*Microbiota/immunology/drug effects
*Bacterial Vaccines/immunology/pharmacology
Staphylococcus epidermidis/immunology/drug effects
Rickettsia/immunology
Tick-Borne Diseases/prevention & control/immunology/microbiology
Female
Vaccines, Subunit/immunology/administration & dosage
Borrelia burgdorferi Group/immunology
Vaccination
Vaccines, Attenuated/immunology/administration & dosage

@article {pmid40134242,
year = {2025},
author = {Trombley, J and Celenza, JL and Frey, SD and Anthony, MA},
title = {Arbuscular Mycorrhizal Fungi Boost Development of an Invasive Brassicaceae.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15508},
pmid = {40134242},
issn = {1365-3040},
support = {//This study was supported by the Dick George Invasives Fund awarded to S.D.F. and M.A.A. M.A.A. was supported by a Vienna Science and Technology Fund (WWTF) Vienna Research Groups for Young Investigators grant awarded to MAA (VRG22-007)./ ; },
abstract = {Invasive plant growth is affected by interactions with arbuscular mycorrhizal fungi (AMF). AMF are mutualists of most land plants but suppress the growth of many plants within the Brassicaceae, a large plant family including many invasive species. Alliaria petiolata (garlic mustard) is a nonnative, nonmycorrhizal Brassicaceae distributed throughout North America in forest understories where native species rely on AMF. If AMF suppress growth of garlic mustard, it may be possible to inoculate AMF to manage invasions. Here, we show that in contrast to expectation, garlic mustard growth nearly doubled in response to AMF inoculation under both laboratory and field conditions. This effect was negatively linked to investments in glucosinolates, a class of defensive compounds. In contrast to typical symbiosis, AMF did not produce arbuscules where nutrient exchange occurs in roots, but AMF inoculation increased plant and soil nitrogen availability. Our findings reveal an adjacent pathway by which AMF promote invasive plant growth without classic symbiotic exchanges. Prior assumptions that garlic mustard suppresses AMF are inadequate to explain invasion success since it benefits from interactions with AMF. This study is the first to demonstrate extensive growth promotion following AMF inoculation in mustard plants, with important implications for invasion biology and agriculture.},
}

@article {pmid40131450,
year = {2025},
author = {Sun, L and Guan, W and Tai, X and Qi, W and Zhang, Y and Ma, Y and Sun, X and Lu, Y and Lin, D},
title = {Research Progress on Microbial Nitrogen Conservation Technology and Mechanism of Microorganisms in Aerobic Composting.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {19},
pmid = {40131450},
issn = {1432-184X},
support = {32160756//National Natural Science Foundation of China/ ; GAUfx-04J03//Fuxi Foundation of Gansu Agricultural University/ ; 23CXNN0007//Gansu Province Science and Technology Plan Project Technology Innovation Guidance Program - LuGan Science and Technology Collaboration topic/ ; 2023-3-66//Science and Technology Plan Project of Lanzhou city/ ; GNKJ-2024-46//Research and Application of Supporting Technologies for Gansu Pig Industry/ ; GAU-XKTD-2022-24//The Discipline Team Project of Gansu Agricultural University/ ; },
mesh = {*Nitrogen/metabolism ; *Composting ; *Manure/microbiology ; *Soil Microbiology ; Livestock/microbiology ; Bacteria/metabolism/genetics/classification ; Aerobiosis ; Animals ; Soil/chemistry ; Microbiota/physiology ; },
abstract = {With economic development and improvements in living standards, the demand for livestock products has steadily increased, resulting in the generation of large amounts of livestock manure, which seriously pollutes the ecological environment and poses a threat to human health. High-temperature aerobic composting is an effective method for treating livestock manure; however, traditional composting processes often lead to considerable nitrogen loss, reduced efficiency of soil conditioners, and increased emissions of harmful gases. The incorporation of physical, chemical, and biological additives can effectively retain nitrogen within the compost. Among these, microbial agents are particularly noteworthy as they precisely regulate the microbial community structure associated with nitrogen transformation during aerobic composting, altering the abundance of functional genes and enzyme activities involved in nitrogen transformation. This approach significantly reduces nitrogen loss and harmful gas emissions. This paper reviews the application effects of microbial agents on nitrogen retention during aerobic composting and explores the underlying regulatory mechanisms, aiming to provide theoretical guidance and new research directions for the application of microbial agents in enhancing nitrogen retention during aerobic composting.},
}

*Nitrogen/metabolism
*Composting
*Manure/microbiology
*Soil Microbiology
Livestock/microbiology
Bacteria/metabolism/genetics/classification
Aerobiosis
Animals
Soil/chemistry
Microbiota/physiology

@article {pmid40129674,
year = {2025},
author = {Hussain, N and Ibrahim Al Haddad, AH and Abbass, S and Alfahl, Z},
title = {The potential impact of habitual sleep quality on glycaemic control and inflammation: A study on geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM).},
journal = {Sleep medicine: X},
volume = {9},
number = {},
pages = {100139},
doi = {10.1016/j.sleepx.2025.100139},
pmid = {40129674},
issn = {2590-1427},
abstract = {Sleep quality and its relationship with glycaemic control is of particular interest in the context of geriatric diabetes. We aimed to investigate the potential impact of habitual sleep quality on glycaemic control status among geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM). A total of 193 geriatric patients recently diagnosed with T2DM in a tertiary-care hospital were selected. A developed questionnaire was used to assess various aspects of sleep quality. Glycaemic control was evaluated through fasting blood glucose levels, HbA1c measurements and number of admissions to the hospital for hypoglycaemic or hyperglycaemic episodes. Patients were divided into Poor Sleep Quality (PSQ, n = 132) and Adequate Sleep Quality (ASQ, n = 61) groups. The PSQ group exhibited significantly worse sleep outcomes, including longer sleep latency (35 ± 9.2 min vs. 15 ± 6.4 min), shorter sleep duration (5 h 42 min vs. 7 h 18 min) and greater use of sleep medications (72 % vs. 22 %). Glycaemic control, measured by HbA1c, was worse in the PSQ group (8.7 ± 1.9 vs. 7.2 ± 1.2; p < 0.01), which also had more frequent severe hypoglycaemic (35 ± 1.4 vs. 8 ± 2.1; p = 0.02) and ketoacidotic episodes (72 ± 1.0 vs. 5 ± 1.1; p = 0.01). These findings suggest an association between poor sleep quality and poorer glycaemic control, with more frequent diabetes-related complications, highlighting the need for further research to explore potential causal relationships and targeted interventions in this population.},
}

@article {pmid40127879,
year = {2025},
author = {Mirsalami, SM and Mirsalami, M},
title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {130},
number = {},
pages = {105738},
doi = {10.1016/j.meegid.2025.105738},
pmid = {40127879},
issn = {1567-7257},
abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.},
}

@article {pmid40121181,
year = {2025},
author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P},
title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf075},
pmid = {40121181},
issn = {1365-2672},
abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.

METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the 3 decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the wood rot/lignin degrading (WRT/LD) community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between Logging Road soils.

CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.},
}

@article {pmid40120670,
year = {2025},
author = {San-Blas, E and Cornejo, MJ and Guerra, M and Olivares, M and Faundez, S and Bastidas, B and Morales-Montero, P and Pizarro, L and Aponte, H and Castañeda-Álvarez, C and Lankin, G},
title = {Where are my nematodes? labelling and visualising entomopathogenic nematodes in vivo using carbon quantum dots.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108317},
doi = {10.1016/j.jip.2025.108317},
pmid = {40120670},
issn = {1096-0805},
abstract = {Identifying single or groups of animals has significantly advanced our understanding of animal biology and ecology. However, labelling is extremely difficult in small animals, like soil invertebrates. Due to the complexity of current methods, the dynamics and interactions of these populations are often studied indirectly. Labelling nematodes or microarthropods such as collembolans or soil acari has been challenging due to the high cost, potential toxicity, genetic modification requirements, cellular processes interference, and photobleaching. In this scenario, no methods can be applied to large numbers of microorganisms at once due to their mentioned practical and biological limitations and cost. In this work we show that quantum carbon dots (Cdots) are effective for labelling infective juveniles (IJs) of entomopathogenic nematodes (EPNs). In in vitro assays the IJs gradually acquired fluorescence, as Cdots accumulated in the lysosome-related organelles from their intestine cells, peaking at day 14, and with no lethal or sub-lethal effects on IJs. Fluorescence was clearly distinguishable from the natural auto-fluorescence of non-labelled IJs and persisted for months in IJs transferred to water. We and non-experts easily differentiated between similar species of EPNs and between two strains of S. feltiae placed in the same matrix (soil or water). We demonstrated for the first time the feasibility of labelling large numbers of IJs (hundreds of thousands/millions) with Cdots at minimal cost without any adverse effects for over a year. Our findings could be the starting point for detailed and large-scale field investigations on nematodes and other small organisms, allowing deeper understanding of their roles in soil ecosystems. This method provides a cost-effective and reliable tool for advancing research in the ecology of soil invertebrates, such as the interactions occurring in communities or between specific organisms, movement and dispersal, population dynamics or ecosystem services in a cryptic environment difficult to study.},
}

@article {pmid40119062,
year = {2025},
author = {Acharya, P and Yegon, MJ and Haferkemper, L and Misteli, B and Griebler, C and Vitecek, S and Attermeyer, K},
title = {Leaf Conditioning and Shredder Activity Shape Microbial Dynamics on Fine Particulate Organic Matter Produced During Decomposition of Different Leaf Litter in Streams.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {18},
pmid = {40119062},
issn = {1432-184X},
mesh = {*Plant Leaves/chemistry ; Animals ; *Particulate Matter/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; Acer/microbiology/chemistry ; Rivers/microbiology/chemistry ; Larva/growth & development ; Fatty Acids/metabolism/analysis ; Fagus/microbiology ; Ecosystem ; Feces/microbiology/chemistry ; Alnus/microbiology/chemistry ; },
abstract = {Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.},
}

*Plant Leaves/chemistry
Animals
*Particulate Matter/analysis
*Bacteria/metabolism/classification
*Microbiota
Acer/microbiology/chemistry
Rivers/microbiology/chemistry
Larva/growth & development
Fatty Acids/metabolism/analysis
Fagus/microbiology
Ecosystem
Feces/microbiology/chemistry
Alnus/microbiology/chemistry

@article {pmid40118512,
year = {2025},
author = {Gomes, IB},
title = {The Overlooked Interaction of Emerging Contaminants and Microbial Communities: A Threat to Ecosystems and Public Health.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf064},
pmid = {40118512},
issn = {1365-2672},
abstract = {Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of "One Health." The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.},
}

@article {pmid40118002,
year = {2025},
author = {Wan, W and Grossart, HP and Wu, QL and Xiong, X and Yuan, W and Zhang, W and Zhang, Q and Liu, W and Yang, Y},
title = {Global meta-analysis deciphering ecological restoration performance of dredging: Divergent variabilities of pollutants and hydrobiontes.},
journal = {Water research},
volume = {280},
number = {},
pages = {123506},
doi = {10.1016/j.watres.2025.123506},
pmid = {40118002},
issn = {1879-2448},
abstract = {Global "Sustainable Development Goals" propose ambitious targets to protect water resource and provide clean water, whereas comprehensive understanding of restoration performance and ecological mechanisms are lacking for dredging adopted for purifying polluted waterbodies and maintaining navigation channels. Here, we conducted a global meta-analysis to estimate ecological restoration consequence of dredging as pollution mitigation and navigation channel maintenance measures using a dataset compiled from 191 articles covering 696 studies and 84 environmental and ecological parameters (e.g., pollutants and hydrobiontes). We confirm that dredging shows negative influences on 77.50% pollutants in the BA model (before dredging vs. after dredging) and 84.21% pollutants in the CI model (control vs. impact) as well as on sediment nutrient fluxes. Additionally, 57.14% attributes (i.e., richness, diversity, biomass, and density) of hydrobiontes in the BA model and 89.47% attributes of hydrobiontes in the CI model responded negatively to dredging. As a result, 76.32% of the pollutants and 61.11% of the hydrobiont attributes responded uniformly to dredging in the BA and CI models. Our findings emphasize that dredging generally decreases pollutants and mitigates algal blooms, controlling phosphorus is easier than controlling nitrogen by dredging, and attributes (i.e., richness, diversity, and biomass) of hydrobiontes (i.e., zooplankton, phytoplankton, and zoobenthos) are density-dependent in dredging-disturbed environments. Our findings broaden our knowledge on ecological restoration performance of dredging as a mitigation measure in global aquatic ecosystems, and these findings might be helpful to use and optimize dredging to efficiently and sustainably purify polluted aquatic ecosystems.},
}

@article {pmid40116066,
year = {2025},
author = {Cusenza, BS and Scelfo, G and Licata, G and Capri, FC and Vicari, F and Alduina, R and Villanova, V},
title = {First Insights Into the Biological and Physical-Chemical Diversity of Various Salt Ponds of Trapani, Sicily.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70075},
doi = {10.1111/1758-2229.70075},
pmid = {40116066},
issn = {1758-2229},
support = {MSCA_0000011//Next Generation EU/ ; },
mesh = {Sicily ; *Ponds/microbiology/chemistry ; *Archaea/classification/genetics/isolation & purification ; *Salinity ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Microbiota ; Phylogeny ; Ecosystem ; Temperature ; Hydrogen-Ion Concentration ; },
abstract = {The salt ponds of Trapani, Sicily, represent an extreme and under-explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical-chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical-chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High-throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter. Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.},
}

Sicily
*Ponds/microbiology/chemistry
*Archaea/classification/genetics/isolation & purification
*Salinity
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Biodiversity
Microbiota
Phylogeny
Ecosystem
Temperature
Hydrogen-Ion Concentration

@article {pmid40113629,
year = {2025},
author = {Moldovan, OT and Levei, E and Ferreira, RL and Silva, MS and Mirea, IC},
title = {Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {17},
pmid = {40113629},
issn = {1432-184X},
support = {PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; GA N°101052342//Biodiversa+, the European Biodiversity Partnership/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Brazil ; *Climate Change ; *Caves/microbiology ; Romania ; Humans ; Microbiota ; Seasons ; Biodiversity ; Tropical Climate ; Ecosystem ; Water Microbiology ; },
abstract = {This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.},
}

*Groundwater/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification
Brazil
*Climate Change
*Caves/microbiology
Romania
Humans
Microbiota
Seasons
Biodiversity
Tropical Climate
Ecosystem
Water Microbiology

@article {pmid40112476,
year = {2025},
author = {Xu, RZ and Cao, JS and Cheng, S and Luo, JY and Ni, BJ and Fang, F and Liu, W and Wang, P},
title = {Heterotrophic nitrification-aerobic denitrification strains: An overlooked microbial interaction nexus in the anaerobic-swing-anoxic-oxic (ASAO) plug-flow system.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {125030},
doi = {10.1016/j.jenvman.2025.125030},
pmid = {40112476},
issn = {1095-8630},
abstract = {This study aims to clarify the overlooked functions of heterotrophic nitrification-aerobic denitrification (HNAD) bacteria in a novel anaerobic-swing-anoxic-oxic (ASAO) continuous plug-flow system. The dissolved oxygen (DO) levels and aerated hydraulic retention time (HRT) varied in the swing zones, providing a more diverse redox environment. High nitrogen (85.0 %) and phosphorus (80.0 %) removal were achieved by enriched HNAD bacteria (e.g., Thauera and Malikia) and phosphate accumulating organisms (PAO, e.g., Rhodocyclus and Azonexus) under middle DO level (1.0-2.0 mg/L) and longer aerated HRT (5.0 h). More importantly, microbial network revealed that HNAD bacteria became a connection point for other functional microorganisms associated with pollutant metabolism, and promoted the cooperation and functional evolution of microbial communities. The microbial ecology analysis captured the high importance of homogeneous selection, diffusion restriction, and drift for microbial community assembly in the ASAO system. Among them, HNAD bacteria contributed to both deterministic and stochastic processes, whereas the community assembly of PAO was mainly affected by the deterministic processes. The upregulation of denitrification genes (i.e., napA, napB, nirS, norB and norC) further confirmed the nitrogen removal contribution of aerobic denitrification by HNAD bacteria. Through this study, a comprehensive analysis of microbial interactions in the ASAO system was achieved, providing valuable insights into the targeted regulation of functional microorganisms in wastewater biological treatment processes.},
}

@article {pmid40112457,
year = {2025},
author = {Liu, J and Xu, G and Zhao, S and He, J},
title = {Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether.},
journal = {Water research},
volume = {280},
number = {},
pages = {123417},
doi = {10.1016/j.watres.2025.123417},
pmid = {40112457},
issn = {1879-2448},
abstract = {Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.},
}

@article {pmid40109964,
year = {2025},
author = {Figueiredo, JEF and Diniz, GFD and Marins, MS and Silva, FC and Ribeiro, VP and Lanza, FE and de Oliveira-Paiva, CA and Cruz-Magalhães, V},
title = {Bacillus velezensis CNPMS-22 as biocontrol agent of pathogenic fungi and plant growth promoter.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1522136},
pmid = {40109964},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.

METHODS: This research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.

RESULTS: CNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.

CONCLUSION: Our findings highlight the CNPMS-22's potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.},
}

@article {pmid40109356,
year = {2025},
author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL},
title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.},
journal = {ACS ES&T engineering},
volume = {5},
number = {3},
pages = {772-781},
pmid = {40109356},
issn = {2690-0645},
abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.},
}

@article {pmid40107140,
year = {2025},
author = {Quattrocelli, P and Piccirillo, C and Kuramae, EE and Pullar, RC and Ercoli, L and Pellegrino, E},
title = {Synergistic interaction of phosphate nanoparticles from fish by-products and phosphate-solubilizing bacterial consortium on maize growth and phosphorus cycling.},
journal = {The Science of the total environment},
volume = {973},
number = {},
pages = {179082},
doi = {10.1016/j.scitotenv.2025.179082},
pmid = {40107140},
issn = {1879-1026},
abstract = {Phosphate nanomaterials, such as hydroxyapatite/β-tricalcium nanoparticles (nHAs) derived from food industry by-products, offer a sustainable alternative to enhance P-use efficiency in agriculture. However, their limited solubility remains a challenge. This study first investigated the mechanisms of P solubilization of salmon and tuna bones (SnHAs and TnHAs) in fifteen strains of phosphate-solubilizing bacteria (PSB) by an in vitro system. Then, best-performing strains were assembled in a consortium and tested in vivo on maize. We hypothesized that combining nHAs and the PSB consortium inoculated as seed coating (SC) outperforms single treatments alone in promoting plant growth and P cycling, and ensures the establishment in plant-soil system without a bacterial reinforcement (BR) by an additional inoculum suspension. The synergistic effect of nHAs and PSB was proved, improving maize root (+22 %) and total plant biomass (+29 %), as well as P (+32 %) and K (66 %) uptake compared to single treatments. With nHAs and SC, P-use efficiency and recovery increased by 25 % and three-fold, respectively, compared to nHAs alone or with bacterial reinforcement. Consistently, root and substrate bacterial biomass were associated with nHAs plus SC, while nHAs alone or with PSB upregulated PHT1;1 and PHT1;2 transporter genes in maize. Finally, linking the in vitro and in vivo system, we demonstrated that propionic acid production and P-solubilization efficiency of PSB co-applied with nHAs are key drivers of maize growth and P uptake. Our findings indicated that co-applying nHAs and PSB through SC offers a sustainable strategy to improve maize P-use efficiency.},
}

@article {pmid40106821,
year = {2025},
author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N},
title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15317},
pmid = {40106821},
issn = {1601-0825},
support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; },
abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.

METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.

RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.

CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.},
}

@article {pmid40106330,
year = {2025},
author = {Maguire, M and DeLappe, N and Clarke, C and Touhy, A and Carlino-MacDonald, U and Hutson, A and Cormican, M and Brennan, W and Devane, G and Morris, D and Coughlan, SC and Miliotis, G and Russo, TA and Burke, LP},
title = {Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001373},
pmid = {40106330},
issn = {2057-5858},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation & purification/classification ; Ireland/epidemiology ; *Klebsiella Infections/microbiology/epidemiology ; Animals ; Virulence/genetics ; *Phylogeny ; Humans ; *beta-Lactamases/genetics ; Retrospective Studies ; Mice ; Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Microbial Sensitivity Tests ; Genomics ; Genotype ; Female ; },
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/isolation & purification/classification
Ireland/epidemiology
*Klebsiella Infections/microbiology/epidemiology
Animals
Virulence/genetics
*Phylogeny
Humans
*beta-Lactamases/genetics
Retrospective Studies
Mice
Bacterial Proteins/genetics
Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Microbial Sensitivity Tests
Genomics
Genotype
Female

@article {pmid40100630,
year = {2025},
author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X},
title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {12},
pages = {e2424463122},
doi = {10.1073/pnas.2424463122},
pmid = {40100630},
issn = {1091-6490},
mesh = {*Bacteria/genetics/metabolism/classification ; *Phylogeny ; *Soil Microbiology ; Microbiota/genetics ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; },
abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.},
}

*Bacteria/genetics/metabolism/classification
*Phylogeny
*Soil Microbiology
Microbiota/genetics
Adaptation, Physiological/genetics
Genome, Bacterial
Evolution, Molecular
Biological Evolution

@article {pmid40099901,
year = {2025},
author = {Lysenko, V and Machushynets, NV and van Dam, JL and Sterk, FAC and Speer, A and Ram, AFJ and Slingerland, CJ and Van Wezel, GP and Martin, NI},
title = {Total Synthesis, Structure Elucidation, and Bioactivity Evaluation of the Cyclic Lipopeptide Natural Product Paenilipoheptin A.},
journal = {Organic letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.orglett.5c00232},
pmid = {40099901},
issn = {1523-7052},
abstract = {In this study, we further investigated the structure of the recently reported cyclic lipopeptide natural product paenilipoheptin A. Here, we disclose the first total synthesis of the compound, allowing for its complete structural assignment. The route developed employs automated SPPS, providing access to the compound in quantities suitable for antibacterial and antifungal testing. These studies unequivocally establish the stereochemical framework of paenilipoheptin A and further reveal that the compound possesses moderate activity against Gram-positive bacteria.},
}

@article {pmid40099871,
year = {2025},
author = {Bittleston, L and Gilbert, J and Klassen, J and Mackelprang, R and Mandel, MJ and Newton, RJ and Paudel, A and Rodriguez-Verdugo, A and Shade, A and Wilhelm, RC and Zhang, Y},
title = {Embracing the systems complexity of microbial ecology and evolution: call for papers.},
journal = {mSystems},
volume = {10},
number = {3},
pages = {e0009125},
doi = {10.1128/msystems.00091-25},
pmid = {40099871},
issn = {2379-5077},
}

@article {pmid40099188,
year = {2025},
author = {Silverio, MP and Schultz, J and Parise, MTD and Parise, D and Viana, MVC and Nogueira, W and Ramos, RTJ and Góes-Neto, A and Azevedo, VAC and Brenig, B and Bonelli, RR and Rosado, AS},
title = {Genomic and phenotypic insight into antimicrobial resistance of Pseudomonas fluorescens from King George Island, Antarctica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535420},
pmid = {40099188},
issn = {1664-302X},
abstract = {The genus Pseudomonas includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, Pseudomonas spp. might act as a reservoir of antimicrobial resistance genes, which have been detected even in isolated environments. The aim of this study was to report the antimicrobial susceptibility profile of 25 Pseudomonas fluorescens isolates from soil samples collected on King George Island (Antarctic Peninsula), and to select non-clonal isolates with unusual phenotypes for whole genome sequencing (WGS). Six classes of antimicrobials were assessed with disk diffusion and colistin with minimum inhibitory concentration (MIC) by broth microdilution. In order to confirm the discrepant phenotypes, MIC by agar dilution was performed for the beta-lactams aztreonam, ceftazidime, cefepime and the aminoglycoside neomycin. The genus Pseudomonas was confirmed by matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF) and the clonal relationships were examined using repetitive extragenic palindromic polymerase chain reaction (BOX-PCR), from which 14 strains were selected for WGS. Antimicrobial susceptibility testing revealed that all strains were susceptible to neomycin and exhibited varying degrees of intermediate or full resistance to aztreonam and colistin. Additionally, 11 strains demonstrated intermediate resistance to ceftazidime, and six were resistant to cefepime. The genomic analysis identified various efflux pumps, predominantly from the ABC transporter and resistance-nodulation-division families. Resistance genes were detected against eight classes of antimicrobials, listed by prevalence: beta-lactams, tetracyclines, polymyxins, aminoglycosides, fosmidomycin, fosfomycin, quinolones, and chloramphenicol. Genes associated with heavy-metal resistance, prophages, and adaptations to extreme environments were also investigated. One notable isolate exhibited not only the highest number of pathogenicity and resistance islands, but also presented a carbapenemase-encoding gene (bla PFM-2) in its genome. Overall, one plasmid was identified in a distinct isolate, which did not exhibit antimicrobial resistance determinants. The genotypic and phenotypic findings are consistent, suggesting that efflux pumps play a critical role in antimicrobial extrusion. This study offers valuable insight into the evolution of antimicrobial resistance in P. fluorescens, particularly in extreme environments, such as Antarctica. By exploring the antimicrobial resistance mechanisms in P. fluorescens, the study sheds light on how isolated ecosystems drive the natural evolution of resistance genes.},
}

@article {pmid40098226,
year = {2025},
author = {Frühe, L and Klein, SG and Angulo-Preckler, C and Martynova, A and Alamoudi, T and García, JVA and Arossa, S and Breavington, J and Frappi, S and Laiolo, E and Lim, KK and Parry, AJ and Re, E and Rosas, DER and Rodrigue, M and Steckbauer, A and Pieribone, VA and Qurban, MA and Duarte, CM},
title = {Particle-Associated Bacterioplankton Communities Across the Red Sea.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70075},
doi = {10.1111/1462-2920.70075},
pmid = {40098226},
issn = {1462-2920},
support = {//National Center of Wildlife/ ; //King Abdullah University of Science and Technology/ ; },
mesh = {Indian Ocean ; *Seawater/microbiology ; *Plankton/genetics/classification ; *Bacteria/genetics/classification/isolation & purification ; Ecosystem ; Microbiota/genetics ; Saudi Arabia ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.},
}

Indian Ocean
*Seawater/microbiology
*Plankton/genetics/classification
*Bacteria/genetics/classification/isolation & purification
Ecosystem
Microbiota/genetics
Saudi Arabia
Phylogeny
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid40097839,
year = {2025},
author = {Blanco, S and Viso, R and Borrego-Ramos, M and López-Flores, R and Mota-Echeandía, D and Tierra, M and Herrero, J and C Castañeda, },
title = {The Ecology of Benthic Diatom Assemblages in Saline Wetlands of the Ebro Basin, NE Spain.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {16},
pmid = {40097839},
issn = {1432-184X},
support = {TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; },
mesh = {*Diatoms/classification/physiology/growth & development ; *Wetlands ; Spain ; *Biodiversity ; Salinity ; Ecosystem ; Electric Conductivity ; },
abstract = {Benthic diatoms play a crucial role in aquatic ecosystems as indicators of environmental conditions and contributors to primary productivity. This study explores the ecology of benthic diatom assemblages in saline wetlands in NE Spain, focusing on the relationships between community parameters, species distributions, and environmental factors, particularly conductivity. Samples were collected from several wetlands representing a range of conductivity and trophic state. A total of 25 diatom taxa were identified, with assemblages dominated by halophilous species. Non-metric multidimensional scaling analysis revealed electrical conductivity (EC) as a primary factor shaping diatom communities, with nutrient levels as a secondary influence. Species exhibited varying responses to the EC gradient, with some showing overlapping niches and others clearly separated. The study found strong correlations between species abundance, occupancy, and their contribution to dissimilarity between sampling sites. More abundant and widespread species were key drivers of community structure and differentiation. Additionally, a significant relationship was observed between taxa occurrence and niche breadth, measured as EC tolerance. Species with broader tolerances tended to have higher occupancy rates, supporting ecological theories about generalist strategies in variable environments. Contrary to some previous research, rare taxa (3-5% in relative abundance) had a negligible effect on assemblage segregation among habitats. The findings suggest that both environmental filtering based on EC tolerance and species' inherent characteristics play important roles in shaping diatom community composition across these saline wetlands. This study contributes to our understanding of diatom ecology in saline habitats and highlights the importance of considering both local abundance and environmental tolerance in ecological studies of these communities. The insights gained can inform more accurate ecological models and improve our understanding of species distribution and community dynamics in saline aquatic ecosystems.},
}

*Diatoms/classification/physiology/growth & development
*Wetlands
Spain
*Biodiversity
Salinity
Ecosystem
Electric Conductivity

@article {pmid40097820,
year = {2025},
author = {Blanchette, RA and Rajtar, NN and Lochridge, AG and Held, BW},
title = {Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9142},
pmid = {40097820},
issn = {2045-2322},
support = {no number//Minnesota Invasive Terrestrial Plants and Pests Center, University of Minnesota/ ; },
mesh = {*Wood/microbiology ; *Fungi/classification/isolation & purification ; Introduced Species ; United States ; Asia ; Phylogeny ; },
abstract = {The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.},
}

*Wood/microbiology
*Fungi/classification/isolation & purification
Introduced Species
United States
Asia
Phylogeny

@article {pmid40097298,
year = {2025},
author = {Morin, C and Alfahl, Z},
title = {A Systematic Review on the Utility of Wastewater Surveillance for Monitoring Yellow Fever Virus and Other Arboviruses.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf066},
pmid = {40097298},
issn = {1365-2672},
abstract = {AIMS: This review aims to examine wastewater surveillance for the detection of Yellow Fever Virus (YFV) and related arboviruses, focusing on concentration and extraction methodology, viral decay kinetics, and quantification techniques.

METHODS: A literature search was conducted across 5 databases: PubMed, Science Direct, Web of Science, Embase, and Google Scholar following the PRISMA guidelines. Studies included were original scientific articles published between April 2014 and April 2024. Human research studies investigating wastewater surveillance and YFV or other arboviruses/flaviviruses were assessed.

RESULTS: 17 studies were included in this review. YFV was not detected in population-based wastewater samples; however, successful detection of similar viruses suggest potential for YFV monitoring with wastewater surveillance. YFV-spiked wastewater studies reveal similar concentration efficiency and decay rates between arboviruses. Effective concentration methods for YFV likely include centrifugation ultrafiltration and solid pellet extraction. YFV and arboviruses decay faster at higher temperatures, though YFV remains detectable for several days at these temperatures.

CONCLUSIONS: Wastewater surveillance presents a promising approach for monitoring YFV and other arboviruses. However, further research is needed to overcome existing limitations and enhance its effectiveness.},
}

@article {pmid40092580,
year = {2025},
author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ},
title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf015},
pmid = {40092580},
issn = {2730-6151},
abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.},
}

@article {pmid40090302,
year = {2025},
author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM},
title = {An efficient strategy for bdd electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137915},
doi = {10.1016/j.jhazmat.2025.137915},
pmid = {40090302},
issn = {1873-3336},
abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.},
}

@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14099},
doi = {10.1111/1755-0998.14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}

@article {pmid40086056,
year = {2025},
author = {Liang, L and Dang, B and Ouyang, X and Zhao, X and Huang, Y and Lin, Y and Cheng, X and Xie, G and Lin, J and Mi, P and Ye, Z and Guleng, B and Cheng, SC},
title = {Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis.},
journal = {International immunopharmacology},
volume = {152},
number = {},
pages = {114408},
doi = {10.1016/j.intimp.2025.114408},
pmid = {40086056},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2[-/-] mice, confirming the role of monocyte recruitment, but persisted in Rag1[-/-] mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.},
}

@article {pmid40085655,
year = {2025},
author = {Muratore, D and Gilbert, NE and LeCleir, GR and Wilhelm, SW and Weitz, JS},
title = {Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {11},
pages = {e2410268122},
doi = {10.1073/pnas.2410268122},
pmid = {40085655},
issn = {1091-6490},
support = {OCE-1829641//National Science Foundation (NSF)/ ; OCE-1829636//National Science Foundation (NSF)/ ; 721231//Simons Foundation (SF)/ ; },
mesh = {*Phosphorus/metabolism ; *Phytoplankton/metabolism ; Ecosystem ; Cyanobacteria/metabolism/genetics ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Oceans and Seas ; Nitrogen/metabolism ; },
abstract = {The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.},
}

*Phosphorus/metabolism
*Phytoplankton/metabolism
Ecosystem
Cyanobacteria/metabolism/genetics
Seawater/microbiology
Bacteria/metabolism/genetics
Oceans and Seas
Nitrogen/metabolism

@article {pmid40085287,
year = {2025},
author = {Micciulla, JL and Baubin, C and Fierer, N},
title = {Effects of Geosmin on the Behavior of Soil Protists.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {14},
pmid = {40085287},
issn = {1432-184X},
support = {2126106//National Science Foundation/ ; 2126106//National Science Foundation/ ; 2126106//National Science Foundation/ ; },
mesh = {*Acanthamoeba castellanii/physiology ; *Soil Microbiology ; *Naphthols/metabolism ; Ciliophora/physiology ; Soil/chemistry/parasitology ; Cercozoa/physiology ; },
abstract = {Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic "earthy" scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing (Streptomyces coelicolor M145) and non-producing (S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists (Cercomonas sp. and A. castellanii) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.},
}

*Acanthamoeba castellanii/physiology
*Soil Microbiology
*Naphthols/metabolism
Ciliophora/physiology
Soil/chemistry/parasitology
Cercozoa/physiology

@article {pmid40085262,
year = {2025},
author = {Castelli, M and Petroni, G},
title = {An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {15},
pmid = {40085262},
issn = {1432-184X},
mesh = {*Phylogeny ; Animals ; *Alphaproteobacteria/genetics/classification/isolation & purification ; Biological Evolution ; Biodiversity ; },
abstract = {The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.},
}

*Phylogeny
Animals
*Alphaproteobacteria/genetics/classification/isolation & purification
Biological Evolution
Biodiversity

@article {pmid40084873,
year = {2025},
author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H},
title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0198924},
doi = {10.1128/spectrum.01989-24},
pmid = {40084873},
issn = {2165-0497},
abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.

IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.},
}

@article {pmid40084850,
year = {2025},
author = {Machushynets, NV and Lysenko, V and Du, C and Slingerland, CJ and Elsayed, SS and Liles, MR and Martin, NI and van Wezel, GP},
title = {Exploring the Chemical Space of Paenibacillus NRPs and Discovery of Paenilipoheptin B.},
journal = {Organic letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.orglett.5c00231},
pmid = {40084850},
issn = {1523-7052},
abstract = {A combination of genomic and metabolomic analyses paired with molecular networking was applied to a collection of Paenibacillus spp. to identify the producers of a little-studied class of lipopeptides known as paenilipoheptins. Mass spectrometry and NMR spectroscopy allowed revision of the structure of previously reported paenilipoheptin A and elucidation of the structure of novel paenilipoheptin B.},
}

@article {pmid40083115,
year = {2025},
author = {Dodds, IL and Watts, EC and Schuster, M and Buscaill, P and Tumas, Y and Holton, NJ and Song, S and Stuttmann, J and Joosten, MHAJ and Bozkurt, T and van der Hoorn, RAL},
title = {Immunity gene silencing increases transient protein expression in Nicotiana benthamiana.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70005},
pmid = {40083115},
issn = {1467-7652},
support = {BB/R017913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S003193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00230/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101019324/ERC_/European Research Council/International ; },
}

@article {pmid40082592,
year = {2025},
author = {Thomas, PW and Kothamasi, D},
title = {Hunting dog behaviour is a key driver impacting harvest quantity and quality of truffles.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8662},
pmid = {40082592},
issn = {2045-2322},
mesh = {Animals ; *Behavior, Animal/physiology ; *Ascomycota/physiology ; Dogs ; Humans ; Seasons ; },
abstract = {Truffles are an iconic food that have long held high regard. Here we explore the seasonality and eco-physiological interactions affecting truffle quality and quantity across time and space. Collaborating with professional truffle hunters working eight different locations, detailed metrics of 3180 recovered truffles from 236 hunt events and spanning a full fruiting period, were recorded. Contrary to expectations, truffle weight showed no correlation with climate variables, suggesting a limited influence of environmental factors such as temperature and precipitation on truffle size. We also found that truffle maturity and damage from mycophagy were strongly linked, with deeper truffles being more mature but also more susceptible to damage. Finally, we observe that scent-dog behaviour significantly impacts the quantity and quality of recovered truffles, and we address the necessity of considering this in truffle ecophysiology studies. Alongside advances in our biological understanding, we make recommendations of how training methods can be improved to lead to greater detection and quality targeting with immediate socioeconomic impact. These findings highlight the complex interplay between truffle physiology, environmental factors, and human and animal behaviours, emphasizing the need for further considered research to enhance our understanding of truffle biology and to improve truffle cultivation practices.},
}

Animals
*Behavior, Animal/physiology
*Ascomycota/physiology
Dogs
Humans
Seasons

@article {pmid40080573,
year = {2025},
author = {Shumilova, O and Sukhodolov, A and Osadcha, N and Oreshchenko, A and Constantinescu, G and Afanasyev, S and Koken, M and Osadchyi, V and Rhoads, B and Tockner, K and Monaghan, MT and Schröder, B and Nabyvanets, J and Wolter, C and Lietytska, O and van de Koppel, J and Magas, N and Jähnig, SC and Lakisova, V and Trokhymenko, G and Venohr, M and Komorin, V and Stepanenko, S and Khilchevskyi, V and Domisch, S and Blettler, M and Gleick, P and De Meester, L and Grossart, HP},
title = {Environmental effects of the Kakhovka Dam destruction by warfare in Ukraine.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6739},
pages = {1181-1186},
doi = {10.1126/science.adn8655},
pmid = {40080573},
issn = {1095-9203},
mesh = {Ukraine ; *Ecosystem ; Geologic Sediments ; Warfare ; Water Supply ; },
abstract = {The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster's spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.},
}

Ukraine
*Ecosystem
Geologic Sediments
Warfare
Water Supply

@article {pmid40080167,
year = {2025},
author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C},
title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {13},
pmid = {40080167},
issn = {1432-184X},
support = {(PFI : 7250A1, Centre de coût : 210F2CVNB)//Institut Français du Caoutchouc/ ; (PFI : 7250A1, Centre de coût : 210F2CVNB)//Institut Français du Caoutchouc/ ; (PFI : 7250A1, Centre de coût : 210F2CVNB)//Institut Français du Caoutchouc/ ; (PFI : 7250A1, Centre de coût : 210F2CVNB)//Institut Français du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; },
mesh = {*Soil Microbiology ; *Hevea/microbiology/growth & development ; Cote d'Ivoire ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; },
abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.},
}

*Soil Microbiology
*Hevea/microbiology/growth & development
Cote d'Ivoire
*Microbiota
*RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Agriculture/methods
RNA, Ribosomal, 18S/genetics

@article {pmid40078544,
year = {2025},
author = {Acciardo, AS and Arnet, M and Gholizadeh Doonechaly, N and Ceccato, A and Rodriguez, P and Tran, HNH and Wenning, Q and Zimmerman, E and Hertrich, M and Brixel, B and Magnabosco, C},
title = {Spatial and temporal groundwater biogeochemical variability help inform subsurface connectivity within a high-altitude Alpine catchment (Riale di Ronco, Switzerland).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1522714},
pmid = {40078544},
issn = {1664-302X},
abstract = {Accessing the deep terrestrial subsurface (greater than 1 km below the surface) presents significant practical challenges, leaving these ecosystems largely uncharacterized despite their extensive presence beneath Earth's landmasses. In this study, we introduce the BedrettoLab Deep Life Observatory (DELOS), a new underground laboratory to study the biogeochemical diversity of groundwater in a high-altitude Alpine catchment tens of meters to 1.6 km underground. Biogeochemical monitoring of DELOS over spatial and temporal scales highlight three dominant ecotypes throughout DELOS: (1) Shallow groundwater with low electrical conductivity enriched in Leptospirillia; (2) High-inflow fault zones enriched in ultra-small bacteria and archaea; (3) Bicarbonate-enriched waters that are enriched in Candidatus Kryptonia and Spirochaetota. Despite a consistent lithology throughout DELOS, groundwater from fractures that are spatially near each other are not always represented by the same ecotype and can be more similar to groundwater emitted from fractures thousands of meters away. Despite this heterogeneity, the biological and hydrochemical compositions of the groundwater of individual fractures remained relatively stable throughout the course of a 1-year monitoring period. An exception to this trend occurred after a series of seismic events near one groundwater-bearing fracture. Here, the microbial community and hydrochemical composition of the groundwater changed after the seismic events but returned to the site's "baseline" composition within 3 weeks. Taken together, these findings provide new insights into the spatial and temporal heterogeneity of deep subsurface ecosystems and the subsurface connectivity of an Alpine subsurface environment.},
}

@article {pmid40077554,
year = {2025},
author = {Smirani, N and Bouazizi, S and Bettaieb, E and Torkhani, R and Hamdi, M},
title = {Effect of Environmentally Friendly Betalain Extraction Methods on Antioxidant Compounds of Tunisian Opuntia stricta Fruit.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/foods14050851},
pmid = {40077554},
issn = {2304-8158},
abstract = {This study focuses on the extraction of betalain compounds from Opuntia stricta as a natural alternative to synthetic colorants and sustainable environmentally friendly technology solutions. Non-conventional extraction technologies including microwave (MW) and ultrasound (US) were used alone or in combination. The extraction process was conducted for both undried Opuntia stricta (OS) and dried Opuntia stricta (DOS) plant material at two distinct drying temperatures, 40 °C and 60 °C, to assess the stability of betalain molecules. The colorant's potential was evaluated by determining the betalain content, total phenolic content, and antioxidant activity. The MW (2 min) and MW (2 min) + US (10 min) extraction processes yielded the greatest betalain content in OS fresh weight (FW), with 48.54 ± 0.29 mg/100 g FW and 51.01 ± 0.16 mg/100 g FW, respectively. Furthermore, the results showed a considerable drop in betalain content when the plant material was dried at 40 °C and 60 °C, with reduction rates of 53.75% and 24.82%, respectively, compared to the betalain content before the drying process. The LC-DAD-ESI-MS analysis supported this result, revealing the presence of 17-decarboxy betanin, 17-decarboxy neobetanin, and Cyclo-dopa5-O-βglucoside in DOS at 40 °C. This study highlights the potential future in the sustainable green extraction of betalain compounds with less heat degradation to offer a stable natural colorant.},
}

@article {pmid40072629,
year = {2025},
author = {Dyczko, D and Szymański, DM and Szymański, D and Kupczak, M and Kolenda, K},
title = {First European record of Rickettsia bellii in Amblyomma rotundatum from Rhinella marina imported to Poland.},
journal = {Experimental & applied acarology},
volume = {94},
number = {3},
pages = {43},
pmid = {40072629},
issn = {1572-9702},
mesh = {Animals ; Poland ; *Rickettsia/isolation & purification ; Female ; *Amblyomma/microbiology/growth & development/physiology ; Tick Infestations/veterinary/parasitology ; },
abstract = {This study reports on the first documented case of Amblyomma rotundatum ticks, a species typically found in the Americas, parasitising an imported toad in Poland. A total of 12 ticks were collected from a single Rhinella marina toad. These ticks were identified as female specimens of A. rotundatum using an examination of morphological characteristics and a molecular analysis. Polymerase chain reaction testing revealed that 75.0% (9/12) of these females were positive for Rickettsia spp. Sequencing of positive samples confirmed the presence of R. bellii. However, no DNA evidence of Borrelia spp. and Anaplasma spp. was detected in the tested ticks. Nevertheless, given the limited number of tick specimens collected from a single host, further research is required to elucidate the pathogen profile of a tick species. This finding represents the second European report of A. rotundatum associated with exported animals, underscoring the importance of vigilance in monitoring the potential spread of ticks and tick-borne pathogens through the global wildlife trade.},
}

Animals
Poland
*Rickettsia/isolation & purification
Female
*Amblyomma/microbiology/growth & development/physiology
Tick Infestations/veterinary/parasitology

@article {pmid40072582,
year = {2025},
author = {Barjau-Aguilar, M and Reyes-Hernández, AMJ and Merino-Ibarra, M and Vilaclara, G and Ramírez-Zierold, JA and Alcántara-Hernández, RJ},
title = {Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {12},
pmid = {40072582},
issn = {1432-184X},
support = {CVU: 747276//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; CVU: 1249011//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; CF-2023-G-155//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; CVU: 41120//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; UNAM, PAPIIT-IN207702//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; UNAM-PAPIIT IN217622//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
mesh = {*Bacteria/genetics/classification/metabolism/isolation & purification ; *Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Tropical Climate ; Fresh Water/microbiology/chemistry ; Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism/analysis ; Phylogeny ; Water Microbiology ; Eutrophication ; },
abstract = {Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3[-] concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.},
}

*Bacteria/genetics/classification/metabolism/isolation & purification
*Archaea/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
*Biodiversity
*Tropical Climate
Fresh Water/microbiology/chemistry
Microbiota
Nitrogen/metabolism
Phosphorus/metabolism/analysis
Phylogeny
Water Microbiology
Eutrophication

@article {pmid40070274,
year = {2025},
author = {Cidan, Y and Wang, J and Wang, H and Xu, C and Zhu, Y and Khan, MK and Basang, W and Li, K},
title = {Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2476539},
doi = {10.1080/10495398.2025.2476539},
pmid = {40070274},
issn = {1532-2378},
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Fungi/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Mycobiome ; },
abstract = {This study aimed to explore the diversity and functions of rumen mycobiota in 14‑ (PLf) and 15‑rib (DLf) Jiani yaks using ITS sequencing. A total of 1,079,105 and 1,086,799 filtered sequences were obtained for the PLf and DLf groups, respectively, with 491 ASVs common to both. No significant difference regarding the α‑diversity of mycobiota within the two groups was observed. While β‑diversity analysis indicated that the abundance of fifteen (15) genera in the PLf group and two (2) genera in the DLf group was found to be significantly different (p < 0.05). 16S rRNA sequencing results indicated that at the phylum level, in 14 ribs yaks Ascomycota, Basidiomycota, and Olpidiomycota, while in 15 rib yaks, Neocallimastigomycota, Mortierellomycota, and Rozellomycota were found to be significantly different (p < 0.05). At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. This study sheds novel insights into how genetic variations influence gut mycobiota in Jiani yak.},
}

Animals
*Rumen/microbiology
Cattle/microbiology
*Fungi/genetics/classification
RNA, Ribosomal, 16S/genetics
Gastrointestinal Microbiome/genetics
Mycobiome

@article {pmid40068413,
year = {2025},
author = {Yang, H and Cappitelli, F and Li, X},
title = {Pollution gradients shape structure and functions of stone heritage bacterial communities at global scale.},
journal = {The Science of the total environment},
volume = {971},
number = {},
pages = {179087},
doi = {10.1016/j.scitotenv.2025.179087},
pmid = {40068413},
issn = {1879-1026},
abstract = {Previous studies mainly focused on the impact of climatic conditions on stone heritage microbial communities, while ignoring a global ecological perspective of pollution on heritage microorganisms. In particular, there is a lack of detailed analysis of the impact of pollution levels on microbial metabolic function. In this study, >6000 bacterial OTUs from 17 world cultural heritage sites were considered. The microbial diversity indexes and potential functions under different pollution levels were analyzed. The results show that particulate matter pollution, such as PM2.5, has an effect on the microbial community in heritage sites comparable to that of temperature and precipitation. High concentrations of particulate matter increased bacterial richness and facilitated the introduction of unique species. Among them, phototrophic bacteria (e.g., Cyanobacteria) and some heterotrophic bacteria (e.g., Actinobacteria and Proteobacteria) formed the core of the microbial community. However, high concentrations of particulate matter reduced the complexity and stability of microbial ecological networks, favoring pollution-tolerant species. Furthermore, elevated particulate concentrations partially suppressed the expression of certain metabolic pathways, particularly genes related to denitrification (e.g., nosZ and nirS). This study reveals the long-term impact of polluted environments on the diversity and potential functions of microbial communities, providing a theoretical basis for developing sustainable strategies for cultural heritage conservation.},
}

@article {pmid40066860,
year = {2025},
author = {Defoirdt, T},
title = {Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2476582},
doi = {10.1080/19490976.2025.2476582},
pmid = {40066860},
issn = {1949-0984},
mesh = {*Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Animals ; },
abstract = {Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.},
}

*Quorum Sensing/drug effects
*Anti-Bacterial Agents/pharmacology
Humans
*Bacteria/drug effects/genetics/metabolism
Drug Resistance, Bacterial
Bacterial Infections/microbiology/drug therapy
Animals

@article {pmid40065660,
year = {2025},
author = {Guislain, ALN and Nejstgaard, JC and Köhler, J and Sperfeld, E and Mischke, U and Skjelbred, B and Grossart, HP and Lyche Solheim, A and Gessner, MO and Berger, SA},
title = {Cell size explains shift in phytoplankton community structure following storm-induced changes in light and nutrients.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70043},
doi = {10.1002/ecy.70043},
pmid = {40065660},
issn = {1939-9170},
support = {731065//European Commission/ ; 871081//European Commission/ ; 01LC1501//German Federal Ministry of Education and Research (BMBF)/ ; GE 1775/2-1//German Research Foundation (DFG)/ ; 603378//the European Commission under its 7th Framework Programme/ ; SAW-2015-IGB-1//Leibniz Association/ ; K45/2017//Leibniz Association/ ; 033L041B//BMBF Infrastructure/ ; },
mesh = {*Phytoplankton/physiology ; Light ; Nutrients ; Animals ; Ecosystem ; Rain ; Lakes ; },
abstract = {Understanding the mechanisms driving community structure and dynamics is crucial in the face of escalating climate change, including increasing incidences of extreme weather. Cell size is a master trait of small organisms that is subject to a trade-off between resistance to grazing and competition for resources, and thus holds potential to explain and predict community dynamics in response to disturbances. Here, we aimed at determining whether cell size can explain shifts in phytoplankton communities following changes in nutrient and light conditions resulting from storm-induced inputs of nutrients and colored dissolved organic matter (cDOM) to deep clearwater lakes. To ensure realistic environmental conditions, we used a crossed gradient design to conduct a large-scale enclosure experiment over 6 weeks. Cell size explained phytoplankton community structure when light availability declined as a result of cDOM supply. Initially unimodal, with small-celled species accounting for up to 60% of the total community biovolume, the cell-size distribution gradually shifted toward large-celled species as light levels declined following cDOM addition. Neither nutrients nor mesozooplankton affected the shift in cell-size distribution. These results suggest a distinct competitive advantage of larger over smaller species at reduced light levels following cDOM inputs during storm events. Importantly, the clustering of species in two distinct size classes implies that interspecific size differences matter as much as cell size per se to understand community dynamics. Given that shifts in cell-size distribution have strong implications for food-web structure and biogeochemical cycles, our results point to the importance of analyzing cell-size distributions of small organisms as an essential element to forecast community and ecosystem dynamics in response to environmental change.},
}

*Phytoplankton/physiology
Light
Nutrients
Animals
Ecosystem
Rain
Lakes

@article {pmid40064943,
year = {2025},
author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC},
title = {GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8214},
pmid = {40064943},
issn = {2045-2322},
support = {3G062519//Fonds Wetenschappelijk Onderzoek/ ; 3G062519//Fonds Wetenschappelijk Onderzoek/ ; 1S51925N//Fonds Wetenschappelijk Onderzoek/ ; 40007505//Excellence Of Science (F.W.O.-F.R.S.-FNRS.)/ ; },
mesh = {Humans ; *Tissue Scaffolds/chemistry ; *Gelatin/chemistry ; *Intestine, Small/cytology/metabolism ; *Epithelial Cells/metabolism ; Caco-2 Cells ; *Hydrogels/chemistry ; Acrylamides/chemistry/pharmacology ; Permeability ; Biocompatible Materials/chemistry ; Cell Survival ; Coculture Techniques ; Cellular Microenvironment ; Cell Adhesion ; Intestinal Mucosa/metabolism/microbiology/cytology ; },
abstract = {Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.},
}

Humans
*Tissue Scaffolds/chemistry
*Gelatin/chemistry
*Intestine, Small/cytology/metabolism
*Epithelial Cells/metabolism
Caco-2 Cells
*Hydrogels/chemistry
Acrylamides/chemistry/pharmacology
Permeability
Biocompatible Materials/chemistry
Cell Survival
Coculture Techniques
Cellular Microenvironment
Cell Adhesion
Intestinal Mucosa/metabolism/microbiology/cytology

@article {pmid40062895,
year = {2025},
author = {McDonald, MD and Lewis, KL and Gentry, TJ},
title = {No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018425},
doi = {10.1128/aem.00184-25},
pmid = {40062895},
issn = {1098-5336},
abstract = {Managing soils in semi-arid agricultural croplands generally focuses on reducing wind erosion, increasing fertility, and storing carbon. Thus, converting conventionally tilled systems to no-tillage and cover-cropped systems are often the first steps towards a conservation management approach across the growing area of semi-arid croplands. From a soil biological perspective, introducing cover crops to semi-arid soils has been shown to alter microbial community structure, which may lead to changes in the biogeochemical pathways expressed in these soils. In this study, we examined the impact of single-species wheat cover cropping and no-tillage on microbial gene expression after 4 and 5 years of implementation. We sequenced the metatranscriptomes of three production systems with varying levels of conservation management: conventional tillage winter fallow, no-tillage winter fallow, and no-tillage with a winter wheat cover crop. Removing tillage was the biggest factor altering microbial gene expression in this study, specifically resulting in upregulation of several photosystem-associated functions. These functions were taxonomically linked to organisms that make up the early stages of biological soil crusts, which may introduce additional benefits to these semi-arid agricultural systems beyond a reduction in wind erosion. Implementing a cover crop did not clearly alter gene expression beyond the effect of tillage removal; however, it did indicate a potential to reduce fungal disease incidence in 1 year of the study. These alterations of microbial activities and selection for potentially beneficial functions should be considered and further studied to aid in maintaining sustainable croplands for our changing climate.IMPORTANCEEliminating tillage from semi-arid agricultural soils has the potential to significantly alter the activities of the soil bacterial community compared with conventionally tilled soils. A major driver of this change was the activities of biological soil crust forming organisms that can provide several environmental benefits to the soil ecosystem beyond the typically associated benefits of conservation management. Furthermore, this study revealed that the implementation of a cover crop regime on no-tillage soils does not confer a major change in the function of the organisms present. Overall, the study reported here reveals that soil management practices aimed at reducing wind erosion and improving sustainability will positively impact the function of the microbial community and suggests that future investigations into the consequences of these functional changes may provide valuable services to these agricultural ecosystems.},
}

@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}

@article {pmid40062764,
year = {2025},
author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K},
title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.},
journal = {Journal of women's health (2002)},
volume = {},
number = {},
pages = {},
doi = {10.1089/jwh.2024.0583},
pmid = {40062764},
issn = {1931-843X},
abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.},
}

@article {pmid40062709,
year = {2025},
author = {Jeong, IJ and Hong, JK and Bae, YJ and Lee, TK},
title = {Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.a.24923},
pmid = {40062709},
issn = {1552-4930},
support = {2020R1C1C100624912//National Research Foundation of Korea/ ; },
abstract = {Although flow cytometry produces reliable results, the data processing from gating to fingerprinting is prone to subjective bias. Here, we integrated autogating with Automated Machine Learning in flow cytometry to enhance the classification of bacterial phenotypes. We analyzed six bacterial strains prevalent in the soil and groundwater-Bacillus subtilis, Burkholderia thailandensis, Corynebacterium glutamicum, Escherichia coli, Pseudomonas putida, and Pseudomonas stutzeri. Using the H2O-AutoML framework, we applied gradient-boosting machine (GBM) models to classify bacteria across different metabolic phases. Our results demonstrated an overall classification accuracy of 82.34% for GBM. Notably, accuracy varied across metabolic phases, with the highest observed during the late log (88.06%), lag (88.43%), and early log phases (89.37%), whereas the stationary phase showed a slightly lower accuracy of 80.73%. P. stutzeri exhibited consistently high sensitivity and specificity across all the phases, which indicated that it was the most distinctly identifiable strain. In contrast, E. coli showed low sensitivity, particularly in the stationary phase, which indicated challenges in its classification. Overall, this study with incorporating autogating and the AutoML framework, substantially reduces subjective biases and enhances the reproducibility and accuracy of microbial classification. Our methodology offers a robust framework for microbial classification in flow cytometric analysis, paving the way for more precise and comprehensive analyses of microbial ecology.},
}

@article {pmid40060716,
year = {2025},
author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y},
title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70994},
pmid = {40060716},
issn = {2045-7758},
abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.},
}

@article {pmid40060289,
year = {2025},
author = {Sarkar, A and Bhattacharjee, S},
title = {Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications.},
journal = {3 Biotech},
volume = {15},
number = {4},
pages = {78},
pmid = {40060289},
issn = {2190-572X},
abstract = {Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.},
}

@article {pmid40060287,
year = {2025},
author = {Maity, A and Das, A and Roy, R and Malik, M and Das, S and Paul, P and Sarker, RK and Sarkar, S and Dasgupta, A and Chakraborty, P and Tribedi, P},
title = {Development of novel strategies against the threats of drug-resistant Escherichia coli: an in silico and in vitro investigation.},
journal = {3 Biotech},
volume = {15},
number = {4},
pages = {77},
pmid = {40060287},
issn = {2190-572X},
abstract = {UNLABELLED: Escherichia coli (E. coli) biofilms pose alarming threats in healthcare due to their invulnerability to drug therapy. Stand-alone therapies of antimicrobial compounds/antibiotics are not particularly effective against those resistant strains. However, combination therapy of compounds could be used to deal with such threats. Towards this direction, the natural compound cuminaldehyde was employed in combination with the aminoglycoside antibiotic tobramycin to target the biofilm-forming multidrug-resistant (MDR) clinical strains of E. coli, which were isolated from urine samples of patient's at Suraksha Diagnostic Private Limited (Kolkata, India). At first, an integrated in silico approach (PASS online, Swiss ADME, PROTOX 3.0, and OSIRIS) was explored to predict the potential biological activities, and other relevant pharmacokinetic parameters of cuminaldehyde and tobramycin. The in silico analysis suggested that tobramycin might not be bioavailable orally due to its molecular size, polarity, and poor GI absorption. However, cuminaldehyde was well absorbed in the GI but could cause irritation if swallowed in LD50 amounts. Further, in vitro assessments were performed to analyse the antimicrobial and antibiofilm activity of both compounds, alone and in combination, against clinical strains of E. coli. The results suggested that cuminaldehyde and tobramycin together could show an additive effect against the clinical strains of E. coli. The combination of the compounds showed a substantial decrease in minimum inhibitory concentration (MIC) and biofilm formation compared to individual application. The present study indicates that combinatorial application involving cuminaldehyde and tobramycin could inhibit the formation of biofilms in E. coli, potentially aiding in the management of microbial infections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04246-0.},
}

@article {pmid40058043,
year = {2025},
author = {Zhong, Q and Santás-Miguel, V and Cruz-Paredes, C and Rousk, J},
title = {Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124883},
doi = {10.1016/j.jenvman.2025.124883},
pmid = {40058043},
issn = {1095-8630},
abstract = {The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg[-1] Cu and 6000 mg kg[-1] tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.},
}

@article {pmid40052378,
year = {2025},
author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H},
title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf055},
pmid = {40052378},
issn = {1365-2672},
abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.

METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied > 50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.

CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.},
}

@article {pmid39883081,
year = {2025},
author = {Shin, GY and Asselin, JA and Smith, A and Aegerter, B and Coutinho, T and Zhao, M and Dutta, B and Mazzone, J and Neupane, R and Gugino, B and Hoepting, C and Khanal, M and Malla, S and Nischwitz, C and Sidhu, J and Burke, AM and Davey, J and Uchanski, M and Derie, ML and du Toit, LJ and Stresow-Cortez, S and Bonasera, JM and Stodghill, P and Kvitko, B},
title = {Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf019},
pmid = {39883081},
issn = {1751-7370},
support = {2019-51181-30013//Specialty Crops Research Initiative Award/ ; //National Institute of Food and Agriculture/ ; //U.S. Department of Agriculture/ ; },
mesh = {*Pantoea/genetics/pathogenicity/isolation & purification ; *Onions/microbiology ; *Plant Diseases/microbiology ; *Plasmids/genetics ; Genome, Bacterial ; Phylogeny ; Multigene Family ; Virulence/genetics ; },
abstract = {Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.},
}

*Pantoea/genetics/pathogenicity/isolation & purification
*Onions/microbiology
*Plant Diseases/microbiology
*Plasmids/genetics
Genome, Bacterial
Phylogeny
Multigene Family
Virulence/genetics

@article {pmid40049093,
year = {2025},
author = {Fonvielle, J and Thuile Bistarelli, L and Tao, Y and Woodhouse, JN and Shatwell, T and Villalba, LA and Berger, SA and Kyba, CCM and Nejstgaard, JC and Jechow, A and Kupprat, F and Stephan, S and Walles, TJW and Wollrab, S and Hölker, F and Dittmar, T and Gessner, MO and Singer, GA and Grossart, HP},
title = {Skyglow increases cyanobacteria abundance and organic matter cycling in lakes.},
journal = {Water research},
volume = {278},
number = {},
pages = {123315},
doi = {10.1016/j.watres.2025.123315},
pmid = {40049093},
issn = {1879-2448},
abstract = {Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.},
}

@article {pmid40048904,
year = {2025},
author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y},
title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.},
journal = {Water research},
volume = {279},
number = {},
pages = {123419},
doi = {10.1016/j.watres.2025.123419},
pmid = {40048904},
issn = {1879-2448},
abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.},
}

@article {pmid40047954,
year = {2025},
author = {Sobhy, IS and Goelen, T and Wäckers, F and Verstrepen, KJ and Wenseleers, T and Jacquemyn, H and Lievens, B},
title = {Impact of Nectar Composition and Nectar Yeasts on Volatile Emissions and Parasitoid Behavior.},
journal = {Journal of chemical ecology},
volume = {51},
number = {2},
pages = {29},
pmid = {40047954},
issn = {1573-1561},
support = {C3 grant (IOF-C32/15/020)//KU Leuven/ ; C3 grant (IOF-C32/15/020)//KU Leuven/ ; C3 grant (IOF-C32/15/020)//KU Leuven/ ; },
mesh = {*Plant Nectar/chemistry/metabolism ; *Volatile Organic Compounds/analysis/metabolism/chemistry ; Animals ; *Metschnikowia/metabolism/physiology/chemistry ; *Aphids/physiology/chemistry ; Female ; *Amino Acids/analysis/metabolism/chemistry ; Fermentation ; Wasps/physiology/chemistry ; Behavior, Animal ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Nectar yeasts can significantly influence the scent of floral nectar and therefore the foraging behavior of flower-visiting insects. While these effects likely depend on nectar chemistry and yeast species, their joint impact on nectar volatile profiles and associated insect responses remain poorly understood. Here, we used four synthetic nectar types varying in sugar and amino acid concentration and two specialist nectar yeasts (Metschnikowia gruessii and Metschnikowia reukaufii) to investigate how nectar composition and yeast species affect volatile profiles and the olfactory responses of the generalist aphid parasitoid Aphidius ervi. Olfactometer assays showed that A. ervi females significantly preferred fermented nectars with high amino acid-low sugar content (HL) and low amino acid-high sugar (LH) content, regardless being fermented by M. gruessii or M. reukaufii, over non-inoculated nectars. This effect was not observed for nectars with low amino acid-low sugar (LL) and high amino acid-high sugar (HH) content. Moreover, LL nectar fermented with M. gruessii became even repellent to the parasitoids. GC-MS analysis of volatile organic compounds (VOCs) revealed that VOC profiles of fermented nectars depended significantly on nectar type (i.e., chemical composition), yeast species, and their interaction. Whereas propyl acetate, isobutyl acetate, styrene, α-guaiene and pentyl-octanoate were associated with the LH fermented nectars, ethyl acetate and E-methyl isoeugenol were mainly associated with the HL fermented nectars, suggesting possible involvement in A. ervi attraction to these nectars. In contrast, isopropyl-hexadecanoate was associated with the non-attractive or repellent LL fermented nectars. Altogether, our results indicate that nectar composition has a strong impact on nectar scent when fermented by specialist nectar yeasts and subsequently on insect foraging behavior.},
}

*Plant Nectar/chemistry/metabolism
*Volatile Organic Compounds/analysis/metabolism/chemistry
Animals
*Metschnikowia/metabolism/physiology/chemistry
*Aphids/physiology/chemistry
Female
*Amino Acids/analysis/metabolism/chemistry
Fermentation
Wasps/physiology/chemistry
Behavior, Animal
Gas Chromatography-Mass Spectrometry

@article {pmid40046987,
year = {2025},
author = {Scott, WT and Rockx, S and Mariën, Q and Regueira, A and Candry, P and Ganigué, R and Koehorst, JJ and Schaap, PJ},
title = {Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {649-660},
pmid = {40046987},
issn = {2001-0370},
abstract = {Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of Clostridia species, such as Clostridium kluyveri, Clostridium autoethanogenum, and Clostridium ljungdahlii. Clostridium luticellarii, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create iSJ444, a constraint-based metabolic model of C. luticellarii using iHN637 of a close relative C. ljungdahlii as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that C. luticellarii maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that C. luticellarii might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of C. luticellarii as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of C. luticellarii to enhance syngas fermentation platforms.},
}

@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}

*Algorithms
*Microbiota
Computational Biology/methods
Bacteria/genetics/classification

@article {pmid40044467,
year = {2025},
author = {Sharma, P and Reitz, T and Singh, SP and Worrich, A and Muehe, EM},
title = {Going beyond improving soil health: cover plants as contaminant removers in agriculture.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.009},
pmid = {40044467},
issn = {1878-4372},
abstract = {Agriculture faces the increasing demands of a growing global population amid simultaneous challenges to soils from climate change and human-induced contamination. Cover plants are vital in sustainable agriculture, contributing to soil health improvement, erosion prevention, and enhanced climate resilience, but their role in contaminant management is underexplored. Herein we review the utilization of cover plants for remediating contaminants such as metals, organic pollutants, nitrate, antibiotics, antimicrobial resistance genes, plastics, and salts. We explore phytoremediation strategies - including phytoextraction, phytodegradation, and phytostabilization - in cover plant management. We highlight the challenges of selecting effective cover plants and the need for biomass removal of non-biodegradable contaminants, and we advocate incorporating phytoremediation concepts into sustainable agricultural management practices beyond nutrient cycling and climate resilience.},
}

@article {pmid40042720,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {14},
pmid = {40042720},
issn = {2197-4365},
abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.},
}

@article {pmid40042690,
year = {2025},
author = {Zhang, T and Wang, XL and Zhou, J and Zhou, W and Zhou, SQ},
title = {Construction of Phosphate-Solubilizing Microbial Consortium and Its Effect on the Remediation of Saline-Alkali Soil.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {11},
pmid = {40042690},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Phosphates/metabolism ; *Soil/chemistry ; *Phosphorus/metabolism ; *Bacteria/metabolism/classification/growth & development ; *Microbial Consortia ; Arachis/microbiology/growth & development/metabolism ; Alkalies/chemistry ; Hydrogen-Ion Concentration ; Calcium Sulfate ; Biomass ; Salinity ; },
abstract = {In this study, phosphate solubilizing bacteria (PSB) with good phosphate-solubilizing capability were isolated from phosphogypsum (PG) storage yard, and phosphate-solubilizing bacteria without antagonistic effect were selected to construct phosphate solubilizing microbial consortium (PSMC), and the synergistic effect of PSMC and PG on the physical and chemical properties of saline-alkali soil, soil enzyme activity, soil bacterial diversity, and the growth index and biomass of peanut plants were explored. The results showed that the effect of phosphorus containing soil amendment on saline-alkali soil was better than that of single PSMC or PG. In the T6 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (6.0 g)), the pH of saline-alkali soil decreased from 8.54 to 7.03, the content of organic matter increased by 6.64%, the content of alkali hydrolyzable nitrogen, available phosphorus and available potassium increased by 81.68%, 60.31%, and 42.03%, respectively, and the activity of alkaline phosphatase increased by 94.95%. In addition, the electrical conductivity value in T4 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (3.0g)) decreased significantly by 20.21%. The diversity and richness of bacterial community in T4 group were the highest, and the growth of peanut plants was the best. The fresh weight of roots and stems increased by 73.34% and 116.6%, respectively. In conclusion, the phosphorus containing soil conditioner prepared by PSMC and PG can effectively improve the soil environment of saline-alkali soil and promote the resource utilization of saline alkali soil.},
}

*Soil Microbiology
*Phosphates/metabolism
*Soil/chemistry
*Phosphorus/metabolism
*Bacteria/metabolism/classification/growth & development
*Microbial Consortia
Arachis/microbiology/growth & development/metabolism
Alkalies/chemistry
Hydrogen-Ion Concentration
Calcium Sulfate
Biomass
Salinity

@article {pmid40042528,
year = {2025},
author = {Zaki, H and Hussein, MA and El-Dawy, EGAM},
title = {Diversity and Symbiotic Associations of Endophytic Fungi in Calotropis procera (Aiton) W.T. Aiton (Asclepiadaceae) Across Three Egyptian Regions: Phenotypic Characterization and Mitotic Activity.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {10},
pmid = {40042528},
issn = {1432-184X},
mesh = {*Endophytes/physiology/isolation & purification/classification ; Egypt ; *Fungi/classification/physiology/isolation & purification ; *Calotropis/microbiology ; *Biodiversity ; *Symbiosis ; Soil Microbiology ; Mitosis ; Phenotype ; },
abstract = {Endophytic fungi are essential contributors to fungal biodiversity, playing key roles in plant defense against pathogens, alleviation of abiotic stress, and promotion of growth. This study conducted a comprehensive survey of the phenotypic characterization of Calotropis procera and its associated endophytic fungi across three regions in Egypt: Qena-Safaga, Qena, and Qena-Kosseir. Positive and significant Pearson correlations among plant morphological traits suggest intrinsic connections. Fungal species diversity exhibited significant variation across the three regions examined. Particularly, the Qena-Kosseir region demonstrated the highest fungal species richness both in soil samples and endophytic fungi. Unique to this region, Allocanariomyces tritici, Aspergillus terreus, Chaetomium globosum, C. murorum, Cladosporium cladosporioides, C. sphaerospermum, Fusarium proliferatum, Penicillium crustosum, P. granulatum, P. spinuloseum, and Roussoella intermedia were identified as endophytes. Additionally, compared to other regions, the Qena-Kosseir area exhibited the presence of Aspergillus fumigatus, A. ochraceus, A. ornatus, A. sclerotiocabonarus, Drechslera halodes, Emericella echinulata, Fusarium oxysporum, and Macrophomina phaseolina in soil samples, underscoring its distinct fungal community composition. Furthermore, antimitotic assays using the Allium cepa test revealed distinct effects of endophytic extracts on various mitotic stages. Of the 33 treatments, 11 showed an increase in the mitotic index (MI), indicating a potential positive effect on plant growth and cell division. This study offers valuable insights into the diversity and functional roles of endophytic fungi associated with C. procera, highlighting their promising applications in sustainable agriculture and plant health management.},
}

*Endophytes/physiology/isolation & purification/classification
Egypt
*Fungi/classification/physiology/isolation & purification
*Calotropis/microbiology
*Biodiversity
*Symbiosis
Soil Microbiology
Mitosis
Phenotype

@article {pmid40042412,
year = {2025},
author = {Hicks, LC and Leizeaga, A and Cruz Paredes, C and Brangarí, AC and Tájmel, D and Wondie, M and Sandén, H and Rousk, J},
title = {Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests.},
journal = {Global change biology},
volume = {31},
number = {3},
pages = {e70065},
pmid = {40042412},
issn = {1365-2486},
support = {2016-06327//Vetenskapsrådet/ ; 2020-03858//Vetenskapsrådet/ ; CTS 22:2131//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 2022-00672//Svenska Forskningsrådet Formas/ ; 2023-02438//Svenska Forskningsrådet Formas/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; },
mesh = {*Droughts ; Ethiopia ; *Climate Change ; *Soil Microbiology ; *Forests ; Soil/chemistry ; Fungi/physiology ; Bacteria ; Microbiota ; Crops, Agricultural/growth & development ; Rain ; },
abstract = {Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.},
}

*Droughts
Ethiopia
*Climate Change
*Soil Microbiology
*Forests
Soil/chemistry
Fungi/physiology
Bacteria
Microbiota
Crops, Agricultural/growth & development
Rain

@article {pmid40042334,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM},
title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156124},
doi = {10.1128/spectrum.01561-24},
pmid = {40042334},
issn = {2165-0497},
abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.},
}

@article {pmid40041707,
year = {2025},
author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q},
title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf025},
pmid = {40041707},
issn = {2730-6151},
abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.},
}

@article {pmid40041702,
year = {2025},
author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H},
title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf002},
pmid = {40041702},
issn = {2730-6151},
abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.},
}

@article {pmid40041671,
year = {2025},
author = {Zernadji, W and Rahmani, F and Jebri, S and Hamdi, M and Khammassi, M and Dhib, S and Hmaied, F},
title = {Distribution of Microbial Contaminants of Minimally Processed Salads Produced in Tunisia: Need to Strengthen Good Hygiene Practices.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {9570620},
pmid = {40041671},
issn = {2314-5765},
abstract = {The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 10[6] CFU/g) and total coliforms (> 10[4] CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81 ± 0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.},
}

@article {pmid40037241,
year = {2025},
author = {Lu, Z and Zeng, J and Wang, L and Zhu, D and Cheng, X and Huang, D and Zhang, J and Yuan, L},
title = {The influence of turbulence caused by hydraulic structures on the community assembly of epilithic biofilms in rivers.},
journal = {Journal of environmental management},
volume = {378},
number = {},
pages = {124645},
doi = {10.1016/j.jenvman.2025.124645},
pmid = {40037241},
issn = {1095-8630},
abstract = {The assembly mechanisms of riverine biofilm communities in river systems represent a central question in aquatic microbial ecology. However, the influence of turbulence on the assembly of generalists and specialists within biofilms remains poorly understood. This study aimed to address this gap by examining a river with multiple spur dikes, using high-throughput sequencing, ecological network analysis, and partial least squares path modeling to explore the assembly process and community structure of biofilms. The results revealed that turbulence intensity (0.029 m/s) and kinetic energy (0.0018 m[2]/s[2]) were significantly higher at the heads of spur dikes compared to the tails. Notably, hydrodynamic parameters explained 6.50% of biofilm community variance, highlighting their underappreciated role as deterministic drivers of microbial assembly. Habitat specialists exhibited heightened sensitivity to hydrodynamic fluctuations, occupying central positions in co-occurrence networks. Additionally, turbulence intensity and kinetic energy emerged as the primary drivers of community assembly, influencing critical ecological processes such as homogeneous selection, drift and dispersal limitation. At the head of spur dikes, a high turbulence region, the weakened impact of homogeneous selection, combined with an increase in dispersal limitation, created conditions that particularly favored habitat generalists. Conversely, low turbulence dike tails supported specialist proliferation via strengthened deterministic selection and nutrient-driven niche partitioning. Furthermore, the partial least squares path modeling confirmed that turbulence dominates the assembly process of microbial specialists and generalists. This study revealed the pivotal role of turbulence in shaping biofilm assembly and driving the spatial differentiation of generalists and specialists, offering fresh insights into the complex interplay between hydrodynamics and microbial ecology in rivers impacted by hydraulic structures. These findings significantly enhance the understanding of biofilm assembly mechanisms and their broader implications for effective river ecosystem management.},
}

@article {pmid40036370,
year = {2025},
author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M},
title = {A specific blend of prebiotics and postbiotics improved gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem (SCIME).},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf056},
pmid = {40036370},
issn = {1525-3163},
abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After two days of stabilization, the 8-day parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites as propionate (donor-dependent), acetate and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with test product compared to control. Repeated supplementation with the test product was therefore able to induce - in vitro - a positive modulation of the microbiome originated from dogs with soft stools.},
}

@article {pmid40035794,
year = {2025},
author = {Vieira, AR and Camacho, F and Sousa, ML and Luelmo, S and Santarém, N and Cordeiro-da-Silva, A and Leão, PN},
title = {The Cyanobacterial Oxadiazine Nocuolin A Shows Broad-Spectrum Toxicity Against Protozoans and the Nematode C. elegans.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {9},
pmid = {40035794},
issn = {1432-184X},
support = {2022.04572.PTDC//Fundação para a Ciência e a Tecnologia/ ; 2022.04572.PTDC//Fundação para a Ciência e a Tecnologia/ ; 2021.04285.CEECIND/CP1663/CT0004//Fundação para a Ciência e a Tecnologia/ ; 952374//Horizon 2020/ ; 952374//Horizon 2020/ ; 952374//Horizon 2020/ ; },
mesh = {Animals ; *Cyanobacteria/metabolism/drug effects ; *Caenorhabditis elegans/drug effects/microbiology ; Dictyostelium/microbiology/drug effects ; Acanthamoeba/drug effects/microbiology ; Antiprotozoal Agents/pharmacology/metabolism ; },
abstract = {Cyanobacteria, known to be rich sources of valuable natural products (NPs) with relevant biological properties, are a unique subject to study the interplay between chemistry and ecology. Cultivation of cyanobacteria as isolated strains may only reveal a small fraction of their NPs. In contrast, investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Cyanobacteria and amoebae are known to co-exist in diverse environments, but the interaction between these organisms has been poorly investigated. Defense strategies against grazer organisms may rely on morphological changes including biofilm formation or increased motility; however, secretion of toxic metabolites seems to be more effective on this regard. Among the most structurally unique cyanobacterial secondary metabolites is nocuolin A, an 1,2,3-oxadiazine metabolite isolated from the cyanobacterial strain Nodularia sp. LEGE 06071 that exhibits potent anti-proliferative activity against several human cancer lines, associated with impairment of mitochondrial oxidative phosphorylation. In this work, we show that nocuolin A is toxic against two well-known model amoebae, Acanthamoeba and Dictyostelium, leading to amoebae encystation and decrease in viability. In addition, in lawn grazing assays, we observed that Nodularia sp. LEGE 06071, the producer strain of nocuolin A, was not grazed by amoeba, while a related strain, which does not produce detectable levels of nocuolin A, was. These results support the possible involvement of nocuolin A as a chemical mediator during the interaction between these organisms. Furthermore, we show that this cyanobacterial metabolite also exhibits potent toxicity against other protozoan organisms and a free-living nematode, making it an interesting broad-spectrum scaffold for the development of antiprotozoal or anti-helminthic drugs.},
}

Animals
*Cyanobacteria/metabolism/drug effects
*Caenorhabditis elegans/drug effects/microbiology
Dictyostelium/microbiology/drug effects
Acanthamoeba/drug effects/microbiology
Antiprotozoal Agents/pharmacology/metabolism

@article {pmid40034844,
year = {2024},
author = {Thompson, MA and Valentine, DL and Peng, X},
title = {Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae028},
pmid = {40034844},
issn = {2633-6685},
abstract = {Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.},
}

@article {pmid40033656,
year = {2025},
author = {Orr, JA and Armitage, DW and Letten, AD},
title = {Coexistence Theory for Microbial Ecology, and Vice Versa.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70072},
doi = {10.1111/1462-2920.70072},
pmid = {40033656},
issn = {1462-2920},
support = {DE230100373//Australian Research Council/ ; DP220103350//Australian Research Council/ ; DE250100656//Australian Research Council/ ; },
mesh = {*Ecology ; Ecosystem ; Microbiota/physiology ; Models, Biological ; Bacteria/classification/genetics ; Microbial Interactions/physiology ; },
abstract = {Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory can be used to disentangle the contributions different mechanisms (e.g., resource partitioning, environmental variability) make to species coexistence. We begin with a short primer on the fundamental concepts of coexistence theory, with an emphasis on the relevance to microbial communities. We next present a systematic review, which highlights the paucity of empirical applications of coexistence theory in microbial systems. In light of this gap, we then identify and discuss ways in which: (i) coexistence theory can help to answer fundamental and applied questions in microbial ecology, particularly in spatio-temporally heterogeneous environments, and (ii) experimental microbial systems can be leveraged to validate and advance coexistence theory. Finally, we address several unique but often surmountable empirical challenges posed by microbial systems, as well as some conceptual limitations. Nevertheless, thoughtful integration of coexistence theory into microbial ecology presents a wealth of opportunities for the advancement of both theoretical and microbial ecology.},
}

*Ecology
Ecosystem
Microbiota/physiology
Models, Biological
Bacteria/classification/genetics
Microbial Interactions/physiology

@article {pmid40028056,
year = {2025},
author = {Vignolle, A and Zehl, M and Kirkegaard, RH and Vignolle, GA and Zotchev, SB},
title = {Secondary Metabolite Biosynthesis Potential of Streptomyces Spp. from the Rhizosphere of Leontopodium nivale Subsp. alpinum.},
journal = {ACS omega},
volume = {10},
number = {7},
pages = {7163-7171},
pmid = {40028056},
issn = {2470-1343},
abstract = {Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeutics. With high rediscovery rates, the attention has shifted to Streptomyces from unique ecological niches for the discovery of new SMs. The plant rhizosphere is one such niche, characterized by complex chemical interactions between the plant and its rhizobiome, which can elicit the production of SMs in Streptomyces. In the present study, 18 Streptomyces strains were previously isolated from the rhizosphere of the rare alpine medicinal plant Leontopodium nivale subsp. alpinum were investigated for their capacity to produce secondary metabolites. Genomes of these strains were analyzed for the presence of SM biosynthetic gene clusters (BGCs). In total, 551 BGCs were detected, of which 217 could not be linked to known SMs. These isolates were cultivated in different media known to support the production of SMs, and 15 out of the 54 methanolic extracts from these cultures exhibited antimicrobial activities. Subsequent liquid chromatography-mass spectrometry analyses of the bioactive extracts led to a putative identification of 69 known SMs as well as 16 potentially new molecules. The results of this study may provide a basis for the discovery of unique molecules with the potential to be developed as drugs against a variety of human diseases.},
}

@article {pmid40025674,
year = {2025},
author = {Abdolahpur Monikh, F and Quik, JTK and Wiesner, MR and Tapparo, A and Pastore, P and Grossart, HP and Akkanen, J and Kortet, R and Kukkonen, JVK},
title = {Importance of Attachment Efficiency in Determining the Fate of PS and PVC Nanoplastic Heteroaggregation with Natural Colloids Using a Multimedia Model.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10918},
pmid = {40025674},
issn = {1520-5851},
abstract = {Here, we assessed the heteroaggregation of polystyrene (PS) and poly(vinyl chloride) (PVC) nanoplastics with SiO2 as a model of natural colloids. Homoaggregation and heteroaggregation were evaluated as a function of CaCl2 (0-100 mM) and natural organic matter (NOM) (50 mg L[-1]) at a designated concentration of nanoplastics (200 μg L[-1]). Critical coagulation concentrations (CCC) of nanoplastics were determined in homoaggregation and heteroaggregation experiments with SiO2 and CaCl2. The attachment efficiency (α) was calculated by quantifying the number of nanoplastics in the presence of CaCl2, NOM, and SiO2 using single-particle inductively coupled plasma mass spectrometry (spICP-MS) and pseudo-first-order kinetics. The calculated α was fed into the SimpleBox4Plastics model to predict the fate of nanoplastics across air, water, soil, and sediment compartments. Nanoplastics exhibited high stability against homoaggregation, while significant heteroaggregation with SiO2 occurred at CaCl2 concentrations above 100 mM. The influence of NOM was also evaluated, showing a reduction in heteroaggregation with SiO2 for both nanoplastic types. Sensitivity analysis indicated that the degradation half-life of the tested nanoplastics had a more significant impact on persistence than did α. The results emphasize the environmental stability of nanoplastics, particularly in freshwater and soil compartments, and the critical role of NOM and emission pathways in determining their fate.},
}

@article {pmid40024538,
year = {2025},
author = {Sliti, A and Kim, RH and Lee, D and Shin, JH},
title = {Whole Genome Sequencing and In Silico Analysis of the Safety and Probiotic Features of Lacticaseibacillus paracasei FMT2 Isolated from Fecal Microbiota Transplantation (FMT) Capsules.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107405},
doi = {10.1016/j.micpath.2025.107405},
pmid = {40024538},
issn = {1096-1208},
abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2,838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3,358 orthologous clusters, including 1,775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.},
}

@article {pmid40022977,
year = {2025},
author = {Noiset, P and Héger, M and Salmon, C and Kwapong, P and Combey, R and Thevan, K and Warrit, N and Rojas-Oropeza, M and Cabirol, N and Zaragoza-Trello, C and Rasmussen, C and Nkoba, K and Vereecken, NJ},
title = {Ecological and evolutionary drivers of stingless bee honey variation at the global scale.},
journal = {The Science of the total environment},
volume = {969},
number = {},
pages = {178945},
doi = {10.1016/j.scitotenv.2025.178945},
pmid = {40022977},
issn = {1879-1026},
abstract = {Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.},
}

@article {pmid40022770,
year = {2025},
author = {Attiani, V and Smidt, H and van der Wielen, PWJJ},
title = {Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment.},
journal = {Water research},
volume = {277},
number = {},
pages = {123328},
doi = {10.1016/j.watres.2025.123328},
pmid = {40022770},
issn = {1879-2448},
abstract = {Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.},
}