Banchi Elisa, Corre Erwan, Del Negro Paola, Celussi Mauro, Malfatti Francesca
National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy.
FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France.
Mar Life Sci Technol. 2023 Nov 3;6(1):126-142. doi: 10.1007/s42995-023-00192-z. eCollection 2024 Feb.
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g, C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.
The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
生活在沉积物中的细菌在海洋生态系统中发挥着重要作用，通过“组学”方法可以更深入地了解这些 largely unexplored organisms 的生态学和生物地球化学。在这里，我们对威尼斯泻湖（亚得里亚海北部）不同子流域的表层沉积物微生物的宏基因组组装基因组（MAGs）进行了表征，这些子流域受到各种自然和人为压力的影响。我们研究了MAGs的生物多样性、主要海洋代谢过程、与人为活动相关的功能、微观尺度的适应性以及生物合成基因簇。从126个MAGs开始，编制了一个包含58个的非冗余数据集，其中大多数（35个）属于（α-和γ-）变形菌门。在广泛的微生物代谢库（包括碳、氮和硫代谢）中，无氧生存的潜力成为最重要的特征之一。混合营养也被发现是一种成功的生存方式。聚类分析表明，不同的MAGs编码相同的代谢模式（例如，碳固定、硫酸盐氧化），因此表明存在代谢冗余。抗生素和有毒化合物抗性基因相互关联，这种情况可能会促进这些遗传特征的传播。MAGs显示出与抗菌和生物技术类别、生物体防御和相互作用以及微量营养素摄取和细胞解毒的适应性策略相关的高生物合成潜力。我们的结果强调，生活在受影响环境中的细菌，如威尼斯泻湖的表层沉积物中的细菌，可能受益于代谢可塑性以及多种次生代谢产物的合成，从而促进生态系统对环境压力的恢复力和稳定性。
在线版本包含可在10.1007/s42995-023-00192-z获取的补充材料。
