Ecological filtering drives rapid spatiotemporal dynamics in fish skin microbiomes

IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Hanna Berggren, Yeşerin Yıldırım, Oscar Nordahl, Per Larsson, Mark Dopson, Petter Tibblin, Daniel Lundin, Jarone Pinhassi, Anders Forsman
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Abstract

Skin microbiomes provide vital functions, yet knowledge about the drivers and processes structuring their species assemblages is limited—especially for non-model organisms. In this study, fish skin microbiome was assessed by high throughput sequencing of amplicon sequence variants from metabarcoding of V3–V4 regions in the 16S rRNA gene on fish hosts subjected to the following experimental manipulations: (i) translocation between fresh and brackish water habitats to investigate the role of environment; (ii) treatment with an antibacterial disinfectant to reboot the microbiome and investigate community assembly and priority effects; and (iii) maintained alone or in pairs to study the role of social environment and inter-host dispersal of microbes. The results revealed that fish skin microbiomes harbour a highly dynamic microbial composition that was distinct from bacterioplankton communities in the ambient water. Microbiome composition first diverged as an effect of translocation to either the brackish or freshwater habitat. When the freshwater individuals were translocated back to brackish water, their microbiome composition converged towards the fish microbiomes in the brackish habitat. In summary, external environmental conditions and individual-specific factors jointly determined the community composition dynamics, whereas inter-host dispersal had negligible effects. The dynamics of the microbiome composition was seemingly non-affected by reboot treatment, pointing towards high resilience to disturbance. The results emphasised the role of inter-individual variability for the unexplained variation found in many host-microbiome systems, although the mechanistic underpinnings remain to be identified.

Abstract Image

生态过滤驱动鱼类皮肤微生物群的快速时空动态变化。
皮肤微生物组具有重要的功能,但有关其物种组合结构的驱动因素和过程的知识却很有限,尤其是对非模式生物而言。在本研究中,通过对鱼类宿主的 16S rRNA 基因 V3-V4 区域代谢编码的扩增子序列变异进行高通量测序,对鱼类皮肤微生物组进行了评估:(i) 在淡水和咸水栖息地之间转移,以研究环境的作用;(ii) 用抗菌消毒剂处理,以重新启动微生物群,并研究群落组装和优先效应;(iii) 单独或成对饲养,以研究社会环境和微生物在宿主间传播的作用。研究结果表明,鱼皮微生物组蕴藏着高度动态的微生物组成,与环境水中的浮游细菌群落截然不同。微生物组的组成首先因转移到咸水或淡水栖息地而发生分化。当淡水个体被转移回咸水后,它们的微生物组组成向咸水生境中的鱼类微生物组靠拢。总之,外部环境条件和个体特异性因素共同决定了群落组成的动态变化,而宿主间的散布影响微乎其微。微生物群组成的动态似乎不受重启处理的影响,这表明微生物群对干扰具有很强的适应能力。研究结果表明,在许多宿主-微生物组系统中发现的无法解释的变异是由个体间变异引起的,但其机理基础仍有待确定。
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来源期刊
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
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