Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada.
Mol Ecol. 2021 Jan;30(2):555-571. doi: 10.1111/mec.15747. Epub 2020 Dec 20.
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
对野生动物微生物组变异的研究通常强调宿主生理学和饮食作为对宿主相关微生物组的近似选择压力。相比之下，微生物传播和生态漂变则较少被考虑。我们使用扩增子测序技术，对成年雌性（n=86）萨布利岛马（加拿大新斯科舍省）的细菌微生物组进行了特征描述，这是对该野生动物种群进行详细个体研究的一部分。我们利用采样日期、马的位置、年龄、父母状况和当地生境变量的数据，对比了时空、生活史和环境因素解释萨布利岛马微生物组多样性的能力。我们通过基于系统发育的和独立于系统发育的零模型方法扩展了这些分析的推断，以确定是否存在偏离随机预期的情况。基于系统发育的多样性衡量指标与空间和当地生境变量相关，但零模型结果表明，生态漂变的异质性，而不是对微生物组的不同选择压力，是这些相关性的原因。相反，基于系统发育的多样性衡量指标与宿主的空间和社会结构最相关，这表明微生物组的分类组成受细菌传播的影响最大。父母状况很重要，但与β-分散度相关，而不是与β-多样性相关（没有幼驹的母马的α多样性较低，微生物组的变异性较大）。我们的研究结果表明，在萨布利岛马种群中，宿主间微生物组的变异主要是由细菌传播和生态漂变驱动的，而不是由不同的选择压力驱动的。这些结果强调了在研究微生物组时需要考虑替代生态过程。
