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Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.
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http://dx.doi.org/10.1007/s12275-023-00063-3 | DOI Listing |
Proc Natl Acad Sci U S A
September 2025
Department of Integrative Biology, University of California, Berkeley, CA 94720-3140.
Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem.
View Article and Find Full Text PDFPLoS Biol
September 2025
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments.
View Article and Find Full Text PDFFEMS Microbiol Ecol
September 2025
School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand, 1142.
The relationship between, and joint selection on, a host and its microbes-the holobiont-can impact evolutionary and ecological outcomes of the host and its microbial community. We develop an agent-based modelling framework for understanding the ecological dynamics of hosts and their microbiomes. Our model incorporates numerous microbial generations per host generation allowing selection on both host and microbes.
View Article and Find Full Text PDFArch Microbiol
September 2025
School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
Endophytic fungi are nonpathogenic fungi that live symbiotically in the interior of healthy plant tissues and form mutualistic associations with their hosts. These fungi are critically involved in promoting plant development, strengthening plant uptake of nutrients, and improving plant resistance to biotic and abiotic stress conditions. Endophytic fungi improve plant growth by synthesizing phytohormones (e.
View Article and Find Full Text PDFAppl Environ Microbiol
September 2025
Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
Unlabelled: The genus includes opportunistic pathogens inhabiting engineered aquatic ecosystems, where managing their presence and abundance is crucial for public health. In these environments, interact positively or negatively with multiple members of the microbial communities. Here, we identified bacteria and compounds with -antagonistic properties.
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