Hou Lei, Zhao Zihao, Steger-Mähnert Barbara, Jiao Nianzhi, Herndl Gerhard J, Zhang Yao
State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
Microbiome. 2025 May 6;13(1):114. doi: 10.1186/s40168-025-02097-8.
Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.
Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).
Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.
海洋雪代表了一个富含有机物的栖息地，并为海洋生态系统中多样的微生物种群提供底物。然而，栖息在海洋雪中的微生物群落内的功能多样性和代谢相互作用在很大程度上仍未得到充分探索，特别是对于参与海洋雪降解的特定代谢途径。在这里，我们使用多组学方法来探索微生物对实验室培养的浮游植物衍生的海洋雪的反应。
我们的结果表明，使用滚动罐系统形成浮游植物衍生的海洋雪后，微生物群落的分类学和功能概况发生了显著变化。响应海洋雪时，宏蛋白质组中微生物代谢过程的变化比宏基因组中更明显。γ-变形菌纲内快速生长的分类群在宏基因组和宏蛋白质组水平上都是最主要的群体。这些γ-变形菌分别拥有多种有助于底物裂解和摄取的碳水化合物活性酶（CAZymes）和转运蛋白。宏基因组组装基因组（MAGs）分析表明，对海洋雪添加物的反应主要由交替单胞菌属、弧菌属和海噬菌属介导。其中，仅表达CAZyme亚家族辅助活性2（AA2）的交替单胞菌在自由生活（FL）和附着在海洋雪上（MA）的微生物群落中都很丰富。因此，交替单胞菌可能在海洋雪的降解中起关键作用。这些交替单胞菌MAGs产生的AA2酶能够将海洋雪分解成较小的聚合物和寡聚物过程中产生的过氧化物中间体解毒，为系统内的其他微生物提供可用底物。此外，弧菌属和海噬菌属MAGs对不同大小级分的海洋雪水解产物表现出不同的反应，表明存在明显的生态位分离。尽管在所有三个MAGs的蛋白质组中都发现趋化蛋白富集，但转运蛋白的差异被确定为导致这两组之间生态位分离的主要因素。FL级分中的弧菌主要利用ATP结合盒转运蛋白（ABCTs），而MA级分中的海噬菌属MAGs主要采用依赖TonB的外膜转运蛋白（TBDTs）。
我们的研究结果揭示了海洋雪降解微生物群落内的基本代谢相互作用，这些群落采用互补的生理机制和生存策略来有效清除海洋雪。这项工作推进了我们对海洋雪归宿以及微生物在海洋碳固存中作用的理解。视频摘要。
