Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia.
FEMS Microbiol Ecol. 2023 Mar 23;99(4). doi: 10.1093/femsec/fiad023.
Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communities sampled with either traditional, composite samples, or small, 1 cm3 cylinders from a discrete location within decomposing European beech (Fagus sylvatica L.) tree trunks. We found that bacterial richness and evenness is lower in small samples when compared to composite samples. There was no significant difference in fungal alpha diversity between different sampling scales, suggesting that visually defined fungal domains are not restricted to a single species. Additionally, we found that composite sampling may obscure variation in community composition and this affects the understanding of microbial associations that are detected. For future experiments in environmental microbiology, we recommend that scale is explicitly considered as a factor and properly selected to correspond with the questions asked. Studies of microbial functions or associations may require samples to be collected at a finer scale than is currently practised.
微生物群落介导的枯木分解和其他环境过程通常采用复合采样策略进行研究，即在较大体积内从多个位置采集枯木，以产生平均微生物群落。在这项研究中，我们使用扩增子测序比较了真菌和细菌群落，这些群落分别采用传统的复合样本或来自分解中的欧洲山毛榉（Fagus sylvatica L.）树干内离散位置的 1cm3 小圆柱体进行采样。我们发现，与复合样本相比，小样本中的细菌丰富度和均匀度较低。不同采样尺度之间的真菌 α 多样性没有显著差异，这表明视觉定义的真菌区不是仅限于一个单一的物种。此外，我们发现复合采样可能掩盖了群落组成的变化，这影响了对检测到的微生物关联的理解。对于环境微生物学的未来实验，我们建议明确考虑规模作为一个因素，并根据提出的问题进行适当选择。研究微生物功能或关联可能需要以比目前更精细的尺度收集样本。
