Gut microbiota are important for the health, fitness and development of animal hosts, but little is known about these assemblages in wild populations of fish. Such knowledge is particularly important for juvenile life stages where nutritional intake critically determines early development, growth, and ultimately recruitment. We characterise the microbiome inhabiting the gut of young-of-the-year European plaice (‘YOY plaice’) on sandy beaches, their key juvenile habitat, and examine how these microbial communities vary spatially in relation to diet and nutritional condition of their plaice hosts. Body size, diet (stomach fullness and eukaryotic 18S ribosomal sequencing), nutritional condition (RNA:DNA) and gut microbiota (16S prokaryotic ribosomal sequencing) were compared in fish at two spatial scales: between beaches separated by 10s of kilometres and between sites at different depths on the same beach, separated by 10s of metres. The main microbial phyla in YOY plaice guts were Proteobacteria, Spirochaetes, Tenericutes and Verrucomicrobiae. Within the Proteobacteria there was an unusual dominance of Alphaproteobacteria. Differences in body size, diet and nutritional condition of YOY plaice between beaches were accompanied by differences in gut microbial assemblage structure. Notably, substantially reduced nutritional condition and size at one of the beaches was associated with lower stomach fullness, reduced consumption of annelids and differences in the abundance and presence of specific microbial taxa. Differences were also detected in microbial assemblages, body size, and diet between depths within the same nursery beach, although stomach fullness and nutritional condition did not vary significantly. The functional links between the environment, gut microbiota, and their hosts are potentially important mediators of the development of young fish through critical life stages. Our study indicates that these links need to be addressed at 10 km and even 10 m scales to capture the variability observed in wild populations of juvenile fish.

肠道微生物群对动物宿主的健康、健康和发育很重要，但对野生鱼类种群中的这些组合知之甚少。这些知识对于幼年生命阶段尤其重要，在这些阶段，营养摄入对早期发育、成长和最终招募至关重要。我们描述了栖息在沙滩上幼年欧洲鲽鱼（'YOY 鲽鱼'）肠道的微生物组，它们是它们的主要幼鱼栖息地，并研究了这些微生物群落如何在空间上与鲽鱼的饮食和营养状况相关主机。在两个空间尺度上比较了鱼的体型、饮食（胃饱度和真核 18S 核糖体测序）、营养状况（RNA：DNA）和肠道微生物群（16S 原核核糖体测序）：在相距数十公里的海滩之间以及在同一海滩上不同深度的地点之间，相距数十米。YOY鲽鱼肠道中的主要微生物门是变形菌门、螺旋体门、细线菌门和疣微菌门。在 Proteobacteria 中，Alphaproteobacteria 占主导地位。海滩之间YOY鲽的体型、饮食和营养状况的差异伴随着肠道微生物组合结构的差异。值得注意的是，其中一个海滩的营养状况和大小大幅降低与胃饱胀度降低、环节动物的消耗量减少以及特定微生物分类群的丰度和存在差异有关。在同一苗圃海滩内不同深度的微生物组合、体型和饮食方面也发现了差异，虽然胃饱胀和营养状况没有显着变化。环境、肠道微生物群及其宿主之间的功能联系是幼鱼通过关键生命阶段发育的潜在重要介质。我们的研究表明，需要在 10 公里甚至 10 米的范围内解决这些联系，以捕捉在幼鱼野生种群中观察到的变异性。