Focardi Amaranta, Bramucci Anna R, Ajani Penelope, Khalil Abeeha, Raina Jean-Baptiste, Seymour Justin R
Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia.
Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
Nat Commun. 2025 Jul 10;16(1):6363. doi: 10.1038/s41467-025-61523-5.
Ecological interactions between phytoplankton and bacteria govern the productivity and biogeochemistry of aquatic ecosystems. However, our understanding of these partnerships primarily comes from laboratory-based model systems, meaning that little is known about the establishment and dynamics of these interactions. Here, we tracked the development of the microbiome of 15 newly isolated phytoplankton species for 400 days. After only 20 days, each phytoplankton harboured a unique bacterial assemblage. Within these assemblages, we identify (i) specialist phytoplankton associates, which are bacteria that establish long-term interactions with 1-2 phytoplankton strains; (ii) generalists, which are associated with 3 or more phytoplankton strains; and (iii) transients, which do not develop sustained associations with any phytoplankton strains. Compared to transients, the generalists and specialists are enriched in genes involved in chemotaxis, vitamin synthesis, secondary metabolite production and the ability to uptake specific phytoplankton-derived compounds. Moreover, generalists display greater potential to move between hosts and release antimicrobials. Finally, examination of co-occurrence patterns in oceanographic time-series revealed that generalists and specialists mirror their phytoplankton partner's abundance in the environment. The divergent genomic characteristics of these discrete bacterial categories highlight different ecological strategies that likely shape phytoplankton microbiomes.
浮游植物与细菌之间的生态相互作用决定着水生生态系统的生产力和生物地球化学过程。然而，我们对这些共生关系的了解主要来自基于实验室的模型系统，这意味着我们对这些相互作用的建立和动态知之甚少。在此，我们对15种新分离的浮游植物物种的微生物组进行了400天的跟踪研究。仅20天后，每种浮游植物就拥有了独特的细菌群落。在这些群落中，我们识别出：（i）专门与浮游植物共生的细菌，即与1 - 2种浮游植物菌株建立长期相互作用的细菌；（ii）兼性共生菌，即与3种或更多浮游植物菌株相关联的细菌；以及（iii）短暂性细菌，即与任何浮游植物菌株都不形成持续关联的细菌。与短暂性细菌相比，兼性共生菌和专门与浮游植物共生的细菌在参与趋化作用、维生素合成、次级代谢产物产生以及摄取特定浮游植物衍生化合物能力的基因方面更为丰富。此外，兼性共生菌在宿主间转移和释放抗菌物质方面具有更大的潜力。最后，对海洋学时间序列中共现模式的研究表明，兼性共生菌和专门与浮游植物共生的细菌反映了其浮游植物伙伴在环境中的丰度。这些不同细菌类别的基因组特征差异突出了可能塑造浮游植物微生物组的不同生态策略。
