Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

由城市地区的活动和扩张引起的河流状况的变化可能会通过增加压力和疾病来影响水生种群，而微生物群可能会发挥重要的中介作用。因此，解开微生物菌群的动态对于更好地理解人为干扰对宿主种群健康和水系统生态完整性的影响至关重要。在此背景下，本研究同时检测了与奥格河（法国）城市化梯度沿线的八种鱼类的粘膜皮肤和肠道组织相关的微生物群落的变化。16S rRNA基因宏条形码显示，皮肤微生物群的结构和组成沿着干扰梯度变化很大，根据鱼类分类学的变化程度较小。Gammaproteobacteria，特别是气单胞菌属的序列，在最城市化地区捕获的鱼占优势，而上游几乎没有。这种机会主义分类群的兴起伴随着系统发育多样性的下降，表明环境压力受到更多限制。相比之下，鱼肠道微生物群随着城市化程度的变化更为温和，可能是因为这个生态位可能较少直接暴露于环境压力因素。共生网络进一步确定了成对的相关细菌分类群，它们随机共存的频率或多或少。皮肤和肠道细菌分类群之间几乎没有相关性，支持这两个微生物生态位是断开的并且不会遭受同样的人为压力脆弱性的假设。