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Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.
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http://dx.doi.org/10.1038/s42003-022-04178-y | DOI Listing |
Front Microbiol
July 2025
Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy.
Introduction: Condensed tannins (CT) influence ruminal microbiota, feed digestibility, and methane emissions, yet their effects in goats are poorly understood.
Methods: This study evaluated the impact of dietary quebracho CT extract at 0%, 2%, 4%, or 6% of dry matter on the composition of the dairy goat ruminal microbiota with a two-times repeated 4 × 4 Latin square design. Bacterial, archaeal, fungal, and protozoan communities were analyzed at the end of each feeding period for relative abundance changes, and their relationship to methane production, nutrient digestibility and feed efficiency were also assessed.
Microbiome
June 2025
State Key Laboratory of Animal Nutrition and Feeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Background: Diurnal oscillations have been reported on ruminal prokaryotes, but the daily rhythmicity of eukaryotes remains unknown. This study investigated diurnal oscillations of ruminal prokaryotes and eukaryotes under three different feeding managements and rumen fluid transplantation conditions, aiming to elucidate the regulatory mechanisms influencing the dynamic shifts of rumen microbiome through the daily feeding cycle.
Results: Quantification and profiling of the microbiota of 288 rumen samples collected from lactating dairy cows (n = 12) every 6-h over 48-h feeding cycles under ad libitum, restricted feeding at daytime and nighttime, respectively, revealed the rhythmicity in the population and abundance of ruminal bacteria, archaea, and protozoa.
FEMS Microbiol Ecol
May 2025
Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany.
Plant-soil feedback and soil microbial legacies play crucial roles in replanting success of apple. This study investigated how different soil amendment strategies influence these factors in replant disease-affected soil. Two approaches were tested: (i) the preculture and amendment of catch crops-either a single species, Tagetes patula, or a diverse catch crop mixture (CCM), and (ii) the inoculation of plant-beneficial microbes-bacteria, arbuscular mycorrhizal fungi, or their combination (SynC).
View Article and Find Full Text PDFPhenomics
February 2025
State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Room C601, No. 2005 Songhu Road, Yangpu District, Shanghai, 200438 China.
Unlabelled: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents.
View Article and Find Full Text PDFBr J Nutr
April 2025
Department of Gastroenterology, School of Translational Medicine, Monash University and Alfred Health, Melbourne, Australia.
The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between.
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