微生物群落形成中的优先效应

一个群落中新物种的形成可能取决于它们到达该群落的顺序和时间，这种现象称为优先效应。来自加利福尼亚大学伯克利分校的主要研究人员在《Nature Reviews Microbiology》综述了优先效应的机制及其在哺乳动物肠道、植物叶际和根际等环境中微生物群落中的重要性。

8 v$ F( b5 E9 R; `- h( ?  _Arrival history influences succession when species that arrive earlier alter resources or environmental conditions in ways that impact species that arrive later, affecting their ability to establish in the community. These interactions, known as priority effects, can generate alternative successional trajectories for whole ecosystems. Researchers from University of California, Berkeley reviewed the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere.
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$ L* U9 Y+ r) @微生物的优先效应机制主要分为三种，包括“抢占生态位”、“促进生态位”和“抑制生态位”。当一个早到物种耗尽系统资源，从而抑制了晚到物种在该群落的建立，这种情况称为“抢占生态位”。“抢占生态位”，特别是营养竞争，是微生物组形成的一个重要过程。当一个早到物种改变环境，有利于另一个晚到物的情况称为“促进生态位”。在微生物群落中，许多菌株可以代谢其他生物的副产品，这些微生物将大的有机分子分解成更小的分子，使得原本无法获得的营养物变得可用，促进后来微生物群落的建立。早到的物种改变了环境状况 (而不是资源水平) 以减缓或阻止晚到物种在该系统的建立，为“抑制生态位”。“抑制生态位”由明显竞争或干扰竞争引起。
Mechanisms of priority effects are divided into Niche pre-emption, Niche facilitative modification and Niche inhibitory modification. Niche pre-emption occurs when an early- arriving organism depletes resources, thereby inhibiting the establishment of a late arriver. Multiple lines of evidence point to niche pre- emption, particularly competition for nutrients (exploitative competition), as an important process in microbiome assembly. Niche facilitative modification (facilitation) occurs when an early- arriving organism alters the environment in a way that benefits a later- arriving organism. Facilitation is also common in microbial communities, where many strains can metabolize byproducts of other organisms. In particular, the ability of arriving microorganisms to establish can depend on the presence of microorganisms that have broken down large organic molecules into smaller molecules, making otherwise inaccessible nutrients available. Niche inhibitory modification (inhibition) occurs when an early- arriving species modifies conditions (rather than resource levels) in a way that slows or prevents the establishment of later- arriving species. Niche inhibitory modification can arise through apparent competition or through interference competition.
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# g' m3 N- _" d& A7 }改变单个菌株或整个菌群的到达顺序的实验研究，可以直接检测微生物群落的优先效应。对植物叶际和小鼠肠道微生物组形成的实验分析显示，大多数观察到的优先效应是抑制作用，只有少数菌株受优先效应的影响表现为促进作用。
- Q$ ?' t4 ~0 zExperimental studies that vary the arrival order of individual strains or entire consortia can directly measure both the role of priority effects in community assembly and the importance of external factors, such as nutrient availability, for these effects. Experimental manipulations of phyllosphere and mouse gut microbiome assembly showed that most observed priority effects were inhibitory, with only a minority of strains benefiting from facilitation.
4 h; K8 v0 s' Y. O8 e" }从全面分析的数据集中最能获得真实微生物群落动态，尤其是涉及稀少和未培养生物类群的相互作用。拥有合适的观察数据集，利用统计方法预测哪些类群是值得研究的，并缩小后续实验验证的研究范围。在一定时间范围内对宿主重复采样可以获取单个生物类群的到达时间和在这个系统的维持时间。如果研究队列足够大，单个生物类群在某系统的维持的变化可能与它们到达之前的该系统原有微生物组组成有关。在不同数据集中，抑制性优先效应总是发生在亲缘关系较近的微生物之间，而不是随机发生的。
# }* R/ r/ a- z. k- r1 {Fully observational datasets have the highest potential to capture realistic microbiome dynamics, especially interactions involving rare and/or uncultured taxa. With an appropriate observational dataset, it is possible to statistically predict which taxa are of interest and narrow the search space for subsequent experimental validation. Repeatedly sampling hosts over time captures the arrival times and subsequent persistence of individual taxa. With sufficient cohort size, the variation in persistence of individual taxa may be linked to resident microbiome composition before their arrival. Across datasets, candidate inhibitory priority effects consistently occurred among more closely related taxa than expected by chance.

                               
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实验室研究和实地调查表明，优先效应是微生物群落组成和功能变化的关键和决定因素。优先效应塑造了微生物群落的形成和稳定性。这表明，在我们开始为人类、牲畜、作物和环境健康重塑微生物群落时，要考虑微生物群落的优先效应。
Laboratory experiments and field surveys point to priority effects as key, understudied determinants of microbiome assembly and function. Overall, the existing data make it clear that priority effects shape microbiome assembly and stability. Therefore, priority effects should be considered as we begin reshaping microbiomes for human, livestock, crop and environmental health.
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