Steiner Leon X, Schmittmann Lara, Rahn Tanja, Lachnit Tim, Jahn Martin T, Hentschel Ute
GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.
GEOMAR Helmholtz Centre for Ocean Research Kiel, RD1 Ocean Circulation and Climate Dynamics, RU Ocean Dynamics, Kiel, Germany.
Environ Microbiome. 2024 Nov 26;19(1):97. doi: 10.1186/s40793-024-00637-7.
Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes.
We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72 h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium.
Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.
噬菌体是已知的环境和宿主相关微生物群落组成及活性的调节因子。然而，单个噬菌体在病毒捕食下对细菌群落动态的影响，及其影响的程度和持续时间，尚未完全明确。在本研究中，我们结合了从波罗的海海绵Halichondria panicea分离出的一种新型海洋噬菌体的形态学和基因组特征，并报告了对天然海绵相关微生物群落进行可控噬菌体操作的首次尝试。
我们使用基于培养和不依赖培养（16S rRNA基因扩增子测序）的方法，研究添加和不添加噬菌体的海绵微生物群落中的细菌群落组成及动态。在可控条件下应用新型的Maribacter专性噬菌体Panino后，我们能够在72小时后检测到微生物群落组成和负荷的全群落变化。在有噬菌体存在的情况下，细菌群落组成随时间变得更加不同，但物种均匀度和丰富度得以维持。噬菌体暴露后，我们观察到常驻微生物群中几个低丰度组成分类单元的丧失，而其他原本代表性不足的分类单元增加。烈性噬菌体可能会引发全群落的干扰，这在通过特定消除组成分类单元导致海绵微生物总谱变化中很明显，这会导致机会性分类单元（如弧菌属、假交替单胞菌属和发光杆菌属）的细菌丰度增加。
我们的研究结果表明，海绵微生物群落的多样性及其恢复力取决于常驻细菌群落成员的维持，无论其丰度如何。噬菌体引发的干扰可通过促进弧菌等机会性细菌的生长并将微生物群落转变为失调状态，从而显著改变群落结构。这些见解突出了噬菌体在塑造微生物群落动态中的作用，并强调了噬菌体在管理海洋宿主相关环境中细菌群落组成方面的应用潜力。
