The digestive tract of animals harbors microbiota important for the host’s fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus’ digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal–bacteria interactions and provides insights into the resilience of the O. gammarellus–associated bacteria to increased flooding frequency.

动物的消化道含有对宿主的健康和表现很重要的微生物群。尽管土壤动物群对生态系统过程很重要，但消化道细菌与土壤动物宿主之间的相互作用仍然没有得到很好的探索。在这项研究中，我们研究了来自以垃圾为食的半陆生甲壳动物Orchestia gammarellus消化道的细菌群落与从环境中获得的细菌群落之间的相互作用。这些生物在盐沼的土壤和植物垃圾中茁壮成长。我们假设海拔是土壤和枯枝落叶细菌群落的重要驱动因素，间接（通过摄入的土壤和枯枝落叶细菌）影响O. gammarellus消化道中的细菌群落. 事实上，我们的研究结果表明，海拔调节土壤和凋落物细菌群落组成以及土壤有机质含量和 C:N 比。土壤和植物凋落物的α多样性指数（丰富度和多样性）不同，植物凋落物的两个指数都随着海拔升高而增加。相比之下，海拔不影响与O. gammarellus消化道相关的细菌群落的组成，这表明宿主进行了选择，尽管在外部来源中也检测到了大部分细菌群落。重要的是，Ca。芽孢杆菌和弧菌在宿主中高度流行和丰富。Ca的分类比较。在不同海拔的宿主中，Bacilloplasma 扩增子序列变异表明由于宿主栖息地（即海洋或半陆地）而导致的系统发育差异，从而支持它们在动物生理学中的潜在功能作用。我们的研究揭示了环境对土壤动物-细菌相互作用的影响，并提供了有关O. gammarellus相关细菌对增加洪水频率的恢复能力的见解。