Mawarda Panji Cahya, van der Kaaij Rens, Dini-Andreote Francisco, Duijker Deniz, Stech Michael, Speksnijder Adrianus Gcl
Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), KST Samaun Sadikun, Bandung, Indonesia.
NPJ Biofilms Microbiomes. 2025 Jun 10;11(1):99. doi: 10.1038/s41522-025-00736-4.
Global biodiversity loss is accelerating due to the transformation of natural landscapes into agricultural and urban areas. Yet, research on the urbanization impact on environmental and host-associated microbiomes, particularly on the ecological processes that mediate their assembly and function, remains scarce. This study investigated the effects of an urbanization gradient on the diversity and assembly processes of the soil microbiome and the microbiomes of three epiphytic lichen species (Candelaria concolor, Physcia adscendens, and Xanthoria parietina). Our findings revealed that the urbanization gradient shaped the soil microbiome, while the lichen microbiomes exhibited strong host specificity and showed no significant changes in diversity along the urbanization gradient. Heterogeneous selection and dispersal limitation primarily governed the soil community assembly and higher community turnover in medium- and highly urbanized zones compared to low-urbanized zones, indicating an increased influence of environmental pressures, altered resources, and habitat fragmentation in more urbanized areas. The lichen microbiome assembly in each species was primarily governed by undominated processes regardless of urbanization level, indicating that both selection and stochasticity contributed to, but neither dominantly influenced, their assembly. The lichen microbiomes further revealed species-specific co-occurrence networks, with microbial compositional signatures and potential functions being essential for lichen fitness and urban ecosystem health. Taken together, our study contributes to understanding how microbial communities are assembled in urban environments, bridging the gap between conceptual theories and empirical findings in the urban ecology of soil and lichen-associated microbiomes.
由于自然景观转变为农业和城市区域，全球生物多样性丧失正在加速。然而，关于城市化对环境微生物群和宿主相关微生物群的影响，特别是对介导其组装和功能的生态过程的研究仍然很少。本研究调查了城市化梯度对土壤微生物群以及三种附生地衣物种（双色蜡盘衣、上攀平茶渍和橙黄网衣）微生物群的多样性和组装过程的影响。我们的研究结果表明，城市化梯度塑造了土壤微生物群，而地衣微生物群表现出很强的宿主特异性，并且沿城市化梯度多样性没有显著变化。与低城市化地区相比，异质性选择和扩散限制主要控制着土壤群落的组装以及中度和高度城市化地区更高的群落周转率，这表明在城市化程度更高的地区，环境压力、资源改变和栖息地破碎化的影响增加。无论城市化水平如何，每个物种的地衣微生物群组装主要由非主导过程控制，这表明选择和随机性都对其组装有贡献，但都不是主要影响因素。地衣微生物群进一步揭示了物种特异性的共现网络，其微生物组成特征和潜在功能对 lichen 适应性和城市生态系统健康至关重要。总之，我们的研究有助于理解微生物群落在城市环境中是如何组装的，弥合了土壤和地衣相关微生物群城市生态学概念理论与实证研究结果之间的差距。
