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The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.
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http://dx.doi.org/10.1007/s00248-025-02493-5 | DOI Listing |
Genome Biol
September 2025
Department of Biology, Plant-Microbe Interactions, Science for Life, Utrecht University, Utrecht, 3584CH, The Netherlands.
Background: Plant roots release root exudates to attract microbes that form root communities, which in turn promote plant health and growth. Root community assembly arises from millions of interactions between microbes and the plant, leading to robust and stable microbial networks. To manage the complexity of natural root microbiomes for research purposes, scientists have developed reductionist approaches using synthetic microbial inocula (SynComs).
View Article and Find Full Text PDFNat Microbiol
September 2025
Division of Computational Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Although dynamical systems models are a powerful tool for analysing microbial ecosystems, challenges in learning these models from complex microbiome datasets and interpreting their outputs limit use. We introduce the Microbial Dynamical Systems Inference Engine 2 (MDSINE2), a Bayesian method that learns compact and interpretable ecosystems-scale dynamical systems models from microbiome timeseries data. Microbial dynamics are modelled as stochastic processes driven by interaction modules, or groups of microbes with similar interaction structure and responses to perturbations, and additionally, noise characteristics of data are modelled.
View Article and Find Full Text PDFProc Biol Sci
September 2025
School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
Insects, such as , rely on innate immune defences to combat microbial threats. Antimicrobial peptides (AMPs) play an important role in limiting pathogen entry and colonization. Despite intensive research into the regulation and biochemical properties of antimicrobial peptides, their exact significance has remained uncertain due to the challenges of mutating small genes.
View Article and Find Full Text PDFInt J Pharm
September 2025
Department of Pharmaceutical Sciences, Via del Liceo 1, 06123 Perugia, Italy. Electronic address:
Indole-3-carboxaldehyde (I3A), a microbial tryptophan metabolite, exhibits significant immunomodulatory activity at the host-microbial interface. However, its rapid transformation into metabolites like indole-3-carboxylic acid (I3CA) raises questions about their therapeutic potential. This study aimed to evaluate the pharmacological contributions of I3CA through the development of a proper delivery strategy.
View Article and Find Full Text PDFEnviron Res
September 2025
National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China. Electronic address: cmm114@mail
Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis.
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